Lorenzo Rosa
email: lorenzo.rosa@unibo.it

Sagar Jha

Ken Birman

DerechoDDS: Efficiently leveraging RDMA for fast and consistent data distribution

Keywords: DDS, RDMA, consistency, performance

Safety-critical applications have always struggled to balance strong consistency with high performance. Kernelbypassing technologies like RDMA (Remote Direct Memory Access) promise to ease this tension by offering fast communication options that can fully leverage modern hardware. We introduce DerechoDDS, an OMG-compliant data distribution service layered over Derecho, an open-source C++ library that combines the consistency guarantees of atomic multicast with the speed of RDMA networks. In adopting this layering, we encountered a significant challenge: DDS is dominated by small messages, whereas Derecho was optimized for large ones. Hence, we identified a set of optimization techniques for small-message atomic multicast over RDMA, obtaining significant performance improvements both for the Derecho library and for DerechoDDS.

I. INTRODUCTION

In safety-critical settings such as automotive or avionics, applications rely on communication middleware solutions to enable fast and robust data distribution. The increasing adoption of IP-based networking even in critical settings makes it possible for applications to leverage standard interfaces such as the OMG Data Distribution Service (DDS) [START_REF]OMG Data Distribution Standard[END_REF], a publishsubscribe middleware specification that guarantees predictable data delivery configurable through QoS policies. The QoS options permit developers to select communication properties matched to the requirements of their applications. For example, an automotive or avionics DDS that will support safety-critical system-management applications for vehicle or aircraft control might require a costly but strongly assured option, whereas a cheaper but less assured QoS level suffices for the passenger entertainment tasks. It is appealing to adopt a single API but then vary the QoS settings as needed.

The DDS communication model is based on the abstraction of a global data space, where topics are represented by objects of a given type. Each application can access the data space via an API that maps a region of local memory. Under the covers, the DDS intercepts updates, sending messages that will replicate the action on remote nodes. QoS options allow the developer to control the level of consistency for each topic: eventual consistency or weak consistency. Under the eventual consistency model, DDS guarantees that all subscribers to the topic will eventually see the same data as in the publisher's local data store. Weak consistency is used when the main goal is low latency and some message loss is acceptable.

In the current OMG standard, there is no way to obtain stronger consistency, such as the classic state machine replication guarantee that every member of a subscriber group will apply the identical updates in the identical order. This reflects a technical limitation at the time the OMG standards were debated: with the prevailing hardware of that period, and the known protocols for achieving stronger properties, the overheads were felt to be too high.

Modern hardware brings this assumption into question. Kernel-bypassing techniques such as Remote Direct Memory Access (RDMA) achieve high throughput (> 200 Gbps) and low latency (∼ 1-2µs), enabling direct data transfers between the virtual memory of processes on remote machines with no operating system involvement and no extra copying. Once available only on supercomputers, today this hardware is an enabling technology for next-generation autonomous systems. Our work begins with the insight that these developments make it feasible to offer stronger DDS QoS options.

This paper presents DerechoDDS, a DDS implementation that leverages RDMA to offer high consistency at high speed. DerechoDDS layers the standard DDS API over a mature, RDMA-capable, open-source library, Derecho [START_REF] Jha | Derecho: Fast state machine replication for cloud services[END_REF], which offers point-to-point and multicast communication options, supporting failure atomicity, total ordering, and optional message logging with durability [START_REF] Jha | Derecho: Fast state machine replication for cloud services[END_REF]. The Derecho protocols have been proved correct using standard techniques and the implementation checked using the Ivy protocol verifier. Derecho can run on fast datacenter TCP but is optimized for RDMA. It sends small messages with one-sided RDMA writes, and large ones in a binomial tree pattern using two-sided RDMA transfers [START_REF]Rdma aware networks programming user manual[END_REF].

Our initial finding was that although highly efficient when exchanging large messages, Derecho was less efficient for small ones. This posed a problem, because most DDS updates are a few KB or less. We microbenchmarked our solution to understand the performance-limiting code paths, then introduced a set of optimization techniques that yielded substantial speedups. Interestingly, the techniques required were quite general, and hence should also be of value in other coordination-based middleware components. They include a new model for coupling application threads to an underlying platform thread, an innovative and highly general form of opportunistic batching, and the use of zero-sized message sends to avoid pauses.

II. DERECHO BACKGROUND

We start with a quick introduction to Derecho. The system was created as a C++ library that can be used to organize a group of processes (nodes) as a distributed service that can execute either on physical servers or in a virtual environment. Derecho manages the group's membership, which evolves through a series of views using partition-free state machine replication. Derecho applications are constructed around "replicated objects," each of which maps to a subgroup consisting of some subset of the top-level group membership. An operation that mutates the state of such an object occurs as a multicast carrying the parameters to the operation, and then will be performed by all replicas.

To support this, Derecho implements a version of Paxos optimized for RDMA, but modified to use the traditional quorum interaction only for membership updates. Data delivery is via atomic multicast, and offers a critical path free of locks and that avoids copying. All messages are delivered to the application by every member in the same order with consistency maintained across failures. Message delivery employs a roundrobin ordering, one message per sender per round, ordered by the sender ordering in the subgroup membership list. Members deliver a message only when every other subgroup member has confirmed its reception. Cleanup after a failure is automatic and transparent: either the operation is completed in the current view, or any pending messages are deleted, and the entire multicast is resent in the next membership view.

Derecho transports data over a data plane, which is implemented differently for large and small messages. In the case of the small messages that arise in Derecho DDS, the key library components are a control layer, modeled as a shared state table (SST), a data layer protocol (Small-Message Multicast, SMC), and a polling framework that orchestrates the two.

Derecho's protocols look quite different from a classic Paxos protocol. A standard Paxos protocol is structured as a 2-phase exchange of information in which a leader proposes a message (or batch of messages) and a delivery "slot", participants respond, and then the leader commits after a quorum is achieved. In Derecho, the same information is shared, but the communication pattern is completely different. Rather than have leaders that make decisions, all nodes exchange status information through the SST using a direct remote memory update to report new events. Every node sees the evolving state of all its peers, and independently deduces protocol progress.

Each node runs a predicate thread that polls a series of predicates, using its local copy of the SST as input, invoking the corresponding triggered code if a predicate is satisfied. For example, if node p has received reports from every node that all messages have been received through message k, p can independently deduce that it is safe to deliver its local copies of the messages up to k in the predetermined roundrobin order. In this example we see how monotonicity is useful in Derecho: SST data is expressed using counters that only increase, booleans that flip from false to true but never back, etc. The consequence is that predicates often can discover a property (such as deliverability) in a single action that may cover multiple messages.

The SMC protocol is the workhorse for DerechoDDS. It manages a set of ring-buffers within the SST: one per sender. To send a message, an application must wait until a slot is free, fill it with relevant data, and then increment a "messages ready" counter. SMC will then issue the corresponding RDMA write to first push the data to the remote subgroup members, and then the counter. Ideally, the size of the buffer (a configuration parameter) should be large enough to avoid senders running out of free slots, thus enabling continuous sending.

Although all of this logic is expressed using predicates, three are of special interest when exchanging small messages. A send predicate detects whether the application has prepared new messages that are ready to be sent. A receive predicate monitors the SMC slots to discover new messages, and the corresponding trigger acknowledges the reception of these messages to the other members. Finally, a delivery predicate checks the SST for messages whose reception has been acknowledged by all the members, and thus are ready to be delivered to the application. The performance of these predicates is crucial for the performance of the applications, hence we targeted them in our optimization work.

III. SMALL MESSAGE OPTIMIZATIONS

As a first step, we evaluated the performance of Derecho with sending patterns and message sizes typical of DDS: messages of up to a few KBs, a few dozen topics with overlapping subgroups. We noticed that the system was unexpectedly slow, and identified three main causes for this poor performance and three optimization techniques to address them. Those solutions turned out to have general applicability in other coordination-based distributed middlewares running on high-speed networks. Due to page-limit constraints, we limit ourselves to a summary.

Opportunistic batching. A key source of inefficiency in SMC was that the latency of sending control data (e.g., acks for receiving a message) is comparable to the latency of sending the application messages themselves. Figure 1 shows that the RDMA write latency for small messages increases only marginally with the data size, rising from 1.73 µs for 1byte data to 2.46 µs for 4KB data. This behavior particularly affects the Derecho predicate thread described in Sec. II, which generates an ack for every new receive and delivery event. Worse, posting each RDMA request to the NIC takes ∼1µs in our setting, a significant delay in light of the critical role of the predicate thread for Derecho. We address this issue by batching events at different stages of the communication pipeline: send, receive and delivery. Instead of letting the system wait to accumulate a fixed-sized batch of messages, which would disrupt performance, we adopt a form of selfbalancing opportunistic batching: a batch can be smaller or larger depending on the number of events a predicate discovers as it loops. For example, the send predicate checks to see if multiple messages are ready. If so, it aggregates them on the fly, and sends a batch. Interestingly, the opportunistic batching of messages or acknowledgments leads to an improvement of both throughput and latency. In contrast, traditional batching mechanisms wait to collect each batch, hurting latency.

Null-send scheme. Recall that Derecho employs a fixed, ordered membership for each epoch, delivering messages in round-robin order by sender. However, this implies that if a sender is not ready to send its next message, the delivery of messages from other senders could be delayed. The problem is that application sending rates might not be steady, and even if they are, delays can be introduced by the OS (e.g., scheduling or interrupt-servicing). To address this issue, we introduce a null-send scheme: when a sender node detects that it is due to send a message but has none ready, it sends a dummy zero-sized message (called null), permitting continued delivery of messages from other senders. In typical DDS use cases, this scheme introduces a negligible bandwidth overhead while making the system adapt very well to real-time delays.

Efficient thread synchronization. Applications access shared data structures when accessing messages or preparing new ones to send. Here, locking protects against concurrency conflicts but can delay the predicate thread. Additionally, many predicates were interleaving accesses to that state (SST) and RDMA write operations. As the latter are costly (they can consume 20-50% of the total predicate time), we refactored the predicate code and placed RDMA operations only at the end. Since the logic of a predicate does not depend on the state at a remote node, but only on what is present in the local SST, it is safe to release locks before proceeding with the time-consuming communication operations. Moreover, this optimization increases batch sizes.

We assess the performance impact of those three optimiza-tions by comparing the optimized system against a baseline version of Derecho protocols. Our performance tests employ an application replicated on an increasing number of nodes (subgroup size from 2 to 16). In one test every member is a sender, whereas there is a single sender in the other test case. Each sender node sends a total of 1 million messages using the new, strongly consistent, QoS option. All members receive every message, and deliver them in the same order.

In this graph we fix the message size at 10KB, but we also evaluated smaller sizes and obtained very similar results.

The tests were executed on our local cluster equipped with 16 physical machines connected with a 12.5GB/s (100Gbps) RDMA Infiniband switch. Each machine has 16 physical cores and 100GB of RAM. Figure 2 plots the results. Overall, we see that Derecho's bandwidth utilization increased from 1GB/s to 9.7GB/s in the "all senders" case, and network utilization improves from 10% to 77.6%. Even with just one sender, where performance declines with the subgroup size due to increased coordination overheads, our optimizations significantly improved both bandwidth and latency.

IV. DERECHODDS

DerechoDDS is a prototype implementation of the OMG DDS API, called Data-Centric Publish-Subscribe (DCPS) [START_REF]OMG Data Distribution Standard[END_REF], which uses Derecho as the underlying communication support. To the best of our knowledge, this is the first attempt to layer the DCPS API on a kernel-bypassing technology like RDMA. Beyond the standard QoS options, DerechoDDS introduces new consistency-related QoS policies to meet the requirements of mission-critical uses, sustaining very high speeds even with the most stringent QoS policy.

Applications use DerechoDDS through the standard DCPS interface. DerechoDDS layers this interface over Derecho by forming a single "top-level" group that includes all publishers and subscribers. The user then defines data types and topics, modeled as subgroups that include only those processes that will publish or subscribe to them. Although our prototype also supports "external clients", nodes that are not in the group but connect through an extra relaying step, space constraints precluded evaluation of that configuration.

DerechoDDS supports a zero-copy data path by allowing developers to build messages "in place," i.e., directly in the memory area that Derecho will write via RDMA. This is crucial: even a single data-copying step would sharply reduce performance on high-speed networks. The system offers four consistency QoS policies. 1. Unordered: This level corresponds to the eventual consistency of the standard DDS. Data is delivered without waiting for stability, and will not be retained after delivery. 2. Atomic multicast: This is layered directly on the Derecho's atomic multicast. Again, data is discarded after delivery. 3. Volatile storage: In addition to the atomic multicast guarantees, the most recent data is retained in receiver memory, allowing late subscribers to catch up. 4.

Persistent storage: Data is additionally appended to a log file on persistent storage for debugging, additional fault tolerance or time-series data analysis. We evaluate the performance of DerechoDDS for a single topic with one publisher and an increasing number of subscribers. We define a Sequence data type representing a byte sequence to be exchanged among the entities. The publisher publishes 1 million samples of the same type, each of 10KB size. Publishers and subscribers are all on different nodes to stress the network performance. Figure 3 shows the bandwidth of DerechoDDS for the offered levels of consistency, running on the optimized version of the Derecho library. Interestingly, we observe that for unordered and atomic multicast mode the performance is very similar, and corresponds to the Derecho atomic multicast performance showed in Figure 2a for the single sender case. This means that the atomic multicast consistency level does not add a significant overhead over the eventually consistent mode. Moreover, that also demonstrates that our DDS implementation is extremely efficient in preserving Derecho's high performance. Speed of the volatile case is limited by memory copying, while the persistent case is limited by DMA data rates to the storage device.

V. RELATED WORK

Traditionally, each application domain defines its own communication middleware: e.g., SOME/IP [START_REF]SOME/IP Protocol Specification[END_REF] is prominent in the automotive community. However, usually these solutions lack the scalability and the extensive QoS support of DDS, which is domain-agnostic and yet integrated with domain-specific platforms, such as AUTOSAR for automotive.

All the major DDS implementations, either commercial or open-source, provide a shared-memory, zero-copy data path to applications co-located on the same host. However, they cannot offer these features for inter-host communication since they use the TCP/IP networking stack. Instead, DerechoDDS leverages RDMA to share memory among remote applications, and relies on the Derecho atomic multicast protocol to offer much stronger consistency guarantees.

The formal model employed by DerechoDDS is discussed in [START_REF] Birman | Communication support for reliable distributed computing[END_REF] and its protocols are proved correct in [START_REF] Jha | Derecho: Fast state machine replication for cloud services[END_REF]. Work on machine-checked proofs (using the Ivy protocol checker and a Coq-based prover) is underway.

A significant part of our work was dedicated to optimizing Derecho for small messages. Prior work on improving performance on RDMA networks was highly influential for systems dominated by one-to-one interactions. In particular, the technique of opportunistic batching was also explored in Kalia et al. [START_REF] Kalia | Using RDMA efficiently for key-value services[END_REF]. However, whereas Kalia focused on one-toone interactions in a key-value storage, DerechoDDS maps to atomic multicast, requiring a more complex approach that optimizes all stages of the communication pipeline.

VI. CONCLUSION

We presented DerechoDDS, an OMG-compliant automotive and avionics data distribution service that leverages modern RDMA hardware to offer a zero-copy data path for publishsubscribe communication among remote hosts. DerechoDDS offers strong consistency guarantees for message delivery order and data durability, as required by safety-critical applications. We obtained these properties by layering the standard OMG DDS interface on top of Derecho, a mature library for state machine replication over RDMA that supports a range of QoS options and employs provably correct Paxosbased protocols. At the outset Derecho was poorly optimized for the DDS traffic pattern, but we successfully improved performance using a set of techniques that should also be broadly useful in other systems that exchange small messages via kernel-bypassing techniques. Finally, we evaluated the performance of a simple DDS application to demonstrate its effectiveness. In the future, we plan to compare DerechoDDS with other DDS implementations, looking at both performance and suitability for mission-critical tasks.

Figure 2 :

 2 Figure 2: Performance of the atomic multicast protocol with one subgroup and 10KB message size, before and after our proposed optimizations.

Figure 3 :

 3 Figure 3: DDS bandwidth for its 4 QoS levels.

  RDMA latency vs data size. Latency remains almost constant for up to 4KB message size.

		12	fully optimized Derecho	all senders		10 4	fully optimized Derecho	all senders
	Bandwidth (GB/s)	2 4 6 8 10	baseline	one sender	Latency (ms)	10 0 10 1 10 2 10 3	baseline	one sender
		Latency (in µs) Figure 1: 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 Subgroup Size 2 10 -1 (a) Average bandwidth utilization for different group sizes. 0	2 2 (b) Average latency for different group sizes 2 4 2 6 2 8 2 10 2 12 2 14 2 16 1.73 2.46 10 20 50 100 200 500 Dominated by minimal wire delay Dominated 2 18 by message size Message size (in Bytes) RDMA writes 3 4 5 6 7 8 9 10 11 12 13 14 Subgroup Size	2 20 15	16

Acknowledgments The authors wish to acknowledge the support received from AFRL/RY (Wright-Patterson), Microsoft, Siemens and Nvidia corporations. We additionally wish to express our gratitude to the anonymous reviewers for their constructive comments and suggestions.


Daouia Moussa

Kheira Senouci

Nori Midoun

Mohamed Lacheheb

Benali Tabeti

Noureddine Benmaarouf

Christophe Hennequin
email: christophe.hennequin-sat@aphp.fr

Genetic diversity of Echinococcus granulosus sensu stricto infecting humans in western Algeria

Abstract:

Human cystic echinococcosis is a zoonosis due to the flat worm Echinococcus granulosus sensu lato. The disease remains a major public health problem in Northern Africa. Molecular typing enables a better understanding of the parasite circulation from animals to humans. In this study we investigated the genotypic diversity of 46 Echinococcus granulosus isolates collected from humans in the western part of Algeria by the mean of partial sequences of 4 mitochondrial loci, namely cox1a, cox1b, nd3 and atp6. Nucleotide polymorphism range from 0.6% (nd3) to 2.7% (cox1a). Eight alleles had not been previously reported. Multilocus analysis showed that all the isolates were from the Echinococcus granulosus sensu stricto (G1 genotype). Nineteen different haplotypes made of the concatenation of 4 sequenced loci were observed, the most common type clustering 13 isolates (36.1%). Twelve of these haplotypes had never been described previously and fifteen (41.7%) haplotypes were represented by only one isolate.

Using sequences from this study and others retrieved from the Genbank database, any clustering either according to the geographic origin within Algeria or according to the human or animal origin of the isolates could be demonstrated supporting that genotype G1 population genetics has been shaped by intensive animal breeding. Keywords: Echinococcus granulosus; cox1; nd3; atp6; mitochondrion; genetic diversity; Algeria.

Introduction

Cystic echinococcosis (CE) is due to the development of the larval stage of the cestode

Echinococcus granulosus sensu lato (s.l.). Human CE is a cosmopolitan zoonosis that represents a major public health problem in endemic countries where collective prophylaxis measures remain insufficient, notably in breeding areas such as North Africa [START_REF] Dakkak | Echinococcosis/hydatidosis: a severe threat in Mediterranean countries[END_REF][START_REF] Eckert | WHO/OIE manual on echinococcosis in humans and animals: a public health problem of global concern[END_REF]. This is the case of Algeria where, despite improved educational hygiene and control over the slaughter of animals, the prevalence of CE remains high, with about 700 cases notified yearly [START_REF] Dakkak | Echinococcosis/hydatidosis: a severe threat in Mediterranean countries[END_REF]. This is due to the domestic life cycle of the parasite where dogs are the predominant definitive host of the parasite and the main source of contamination for humans, while intermediate hosts are represented by various species of ruminants. Previous reports from Algeria have shown that16 to 42% of stray-dogs harbor E. granulosus s.l. in their intestine [START_REF] Bentounsi | Cestodes of Untreated Large Stray Dog Populations in Algeria: A Reservoir for Herbivore and Human Parasitic Diseases[END_REF], and that sheep, goat, cattle, horses, dromedaries, and wild boars can act as intermediate hosts, sheep being by far the most common (Bardonnet et al. 2003;[START_REF] Eckert | WHO/OIE manual on echinococcosis in humans and animals: a public health problem of global concern[END_REF][START_REF] Kouidri | Comparative Study on Fertility, Viability and Biochemical Profiles of Hydatid Cyst Fluid from the Lungs and Liver of Sheep in Algeria[END_REF][START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF] Maillard | Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF].

A high degree of genetic diversity has been documented in E. granulosus s.l. that partly correlates with intermediate host susceptibility (Alvarez Rojas et al. 2014;[START_REF] Romig | Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato[END_REF].

According to the current nomenclature, Echinococcus granulosus s.l. is now considered a species complex that includes Echinococcus granulosus sensu stricto (s.s.), Echinococcus equinus, Echinococcus ortleppi, Echinococcus felidis and Echinococcus canadensis (Alvarez [START_REF] Rojas | Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge[END_REF][START_REF] Romig | Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato[END_REF]. E. granulosus s.s. is the predominant species in many regions of the world, while E. canadensis, G6/G7 and, G8, G10 genotypes are dominant in eastern and north of Europe, respectively (Alvarez [START_REF] Rojas | Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge[END_REF]). E. granulosus s.s. includes 2 genotypes denoted G1 and G3, G2 being now considered a microvariant of G3 [START_REF] Kinkar | New mitogenome and nuclear evidence on the phylogeny and taxonomy of the highly zoonotic tapeworm Echinococcus granulosus sensu stricto[END_REF]. The G1 genotype is predominant in all intermediate hosts, including Humans and is widely found in cattle in North Africa (Alvarez Rojas et al. 2014;[START_REF] Deplazes | Global Distribution of Alveolar and Cystic Echinococcosis[END_REF]). G3, initially identified from water buffalo, can also infect other intermediate hosts including

Humans [START_REF] Romig | Taxonomy and molecular epidemiology of Echinococcus granulosus sensu lato[END_REF].

Despite the importance of this public health problem in Algeria, epidemiological studies, and particularly molecular epidemiological studies, focused on E. granulosus s.l. from this country are still scarce. They conclude on the predominance of the E. granulosus s.s. G1 genotype as the main source of human infections (Bardonnet et al. 2003;[START_REF] Maillard | Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]. Some of these surveys may have limited conclusion notably due to length of the nucleotide sequence analyzed. However, such studies are important for different purposes.

Even considering that the genotype is not strictly restricted to one intermediate host, the identification of the predominant species in a region would help health authorities to drive their prevention measures. Results of such studies can also give light on the circulation of the parasite between different regions, and to analyze the different hosts involved, including humans.

To increase our knowledge on the genetic diversity of E. granulosus s.l. circulating in Algeria, we initiated a genotyping study based on a 4 partial mitochondrial loci system focused on human isolates from the Western part of Algeria, where sheep breeding is mostly intensive.

Materials and methods

Biological samples

Fluid from of 46 hydatid cysts (19 pulmonary and 27 hepatic) obtained after surgical resection from 45 patients admitted at the Hospital of Oran (EHU) were available for the genotyping study (Online Resource 1). Patients were from different localities mainly in the north-west of Algeria (Figure S1). Fluids were first stored in 0.9% sodium chloride solution to avoid protoscolex desiccation. They were then centrifuged at 50xg for 5min and the pellet containing protoscolex and/or the germinal layer were stored at -20°C in 90% ethanol for further analysis.

Molecular analysis

DNA extraction

DNA was extracted from hydatid tissue samples (protoscolex and/or germinal layer) using a mechanical disruption (MagnaLyser, Roche) followed by column-based extraction (QIAamp DNA Blood kit, Qiagen) according to the manufacturer's instructions.

Amplification and direct sequencing

Four mitochondrial fragments were selected for genotyping (Figure S2). They target the cytochrome c oxidase subunit 1 (2 fragments referred as cox1a and cox1b), the dehydrogenase subunit 3 (nd3) and the ATPase subunit 6 (atp6). Briefly, amplification was performed with a mixture containing 0.3 U Taq polymerase (Taq Gold, Invitrogen), 1µM forward and reverse primers and 5 µl DNA in a final volume of 25 µl. Primers have been previously described and their sequences are available in Online Resource 2 [START_REF] Bowles | Genetic variants within the genus Echinococcus identified by mitochondrial DNA sequencing[END_REF][START_REF] Lavikainen | Molecular characterization of Echinococcus isolates of cervid origin from Finland and Sweden[END_REF].

For all the targets, amplification was achieved according to the following thermal program: 10 min at 94 °C, followed by 35 cycles of denaturation at 94°C; hybridization at 50°C and elongation at 72°C, each of these steps lasted 30 sec; then a final extension at 72 °C during 10 min. Amplification was checked by running a 1% agarose gel electrophoresis. PCR products were then purified (QIAquick PCR Purification kit) and subjected to direct sequencing with the BigDye Terminator v3.1 reagent (Invitrogen), according to the manufacturer's protocol and using the primers used for amplification. The corresponding chromatograms were obtained using the 3500×l Dx Genetic Analyzer automatic sequencer.

Phylogenetic analysis

The sense and anti-sense chromatograms were aligned and manually edited using the BioEdit software version 7.2.6.Consensus sequences were then compared by the mean of the Blastn program available on the National Center for Biotechnology Information website (https://blast.ncbi.nlm.nih.gov/). Single locus multiple alignments were performed including the reference mitochondrion genome (Genbank accession number AB786664) published by [START_REF] Nakao | Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes[END_REF])and using the MegaX (vs 10.1.8) software with the Clustal algorithm.

Phylogenetic analysis was achieved using these sequences and sequences available in Genbank and corresponding to Algerian E. granulosus s.s. isolates (Bardonnet et al. 2003;[START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF][START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF] Maillard | Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]. We performed both an analysis using the cox1blocus because a higher number of sequences are available in Genbank with 100% query cover and another one using the concatenated sequences of the 4 loci further in called haplotypes, obtained in our study. The phylogenetic relationship between sequences identified in our series and sequences retrieved in Genbank was illustrated by the construction of minimum spanning trees using an optimal eBurst algorithm [START_REF] Francisco | Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach[END_REF]). Graphical representation was done using the Phyloviz online program (http://www.phyloviz.net/).In this graphical representation, isolates with the same allelic profile fall in the same circle, the size of which is proportional to the number of isolates with that particular profile.

The protocol has been approved by the Ethics Committee of the Hospital of Oran (ref. CA O2/2020). Patients were informed during their hospital stay that data from their medical charts could be used in a medical study that would be possibly published in a scientific journal. At the beginning of the study, each specimen was given a code and all the experiments were performed without knowledge of the patients' information, so that anonymization did not allow their identification.

Results

Amplification failed for the 4 genetic targets for two specimens. Positive amplification and sequencing were obtained for 37, 42, 43 and 43isolates for atp6, nd3, cox1a, cox1b, respectively making complete haplotype available for 36 isolates.

Single locus analysis revealed 8, 3, 10, 6allelesfor locus 1 to 4, respectively (Table 1). The level of diversity with highest for cox1a locus (2.7%) and lowest for nd3 locus (0.6%). Eight of these alleles have not been reported previously and have been deposited in GenBank (from MW417352 to MW417359 and MW446898-MW446899).

Phylogenetic analysis of concatenated sequences from our study and those found in GenBank showed that all our isolates were of E. granulosus s.s. G1 genotype (data not shown). Multilocus analysis on the 36 isolates with a complete haplotype allowed the differentiation of 19haplotypes named Hap01 to Hap19 (Table 2). Hap01 was the most common type isolates (36.1%). Twelve of these haplotypes had never been reported previously and fifteen (41.7%) haplotypes were represented by only one isolate. Notably 56% of the pulmonary isolates had unique haplotype versus 20% for hepatic isolates.

The first phylogenetic tree was based on the cox1b locus taking the advantage of 92homolog sequences in GenBank [START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF][START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]. It shows that 36 (83.7%) of our isolates harbor the predominant sequence (cox1b_01), similar to the reference mitochondrial genome. Sequences from all the isolates but 2 were also direct satellites from this central clade with links corresponding to a single nucleotide mutation. No segregation according to the host nor to the geographic origin could be demonstrated (Fig1a,Fig 1b). When using complete concatenated haplotypes using the sequences of four loci tested in our study, Hap01 appeared as the founder, giving birth to closely related haplotypes either tested in this study or retrieved in Genbank. However, Hap10, which originated indirectly from Hap01 (2 nucleotide mutations), forms a second cluster distantly with further diversification (Figure 2).

Discussion

Because the life cycle of E. granulosus s.l. includes domestic animals, mainly dogs and livestock, eradication of CE can be reached by control measures that could be set up from data obtained in epidemiological surveys. There are several studies focused on the genetic diversity of E. granulosus s.l. conducted in the Maghreb but those conducted in Algeria are more rare (Bardonnet et al. 2003;[START_REF] Boufana | Genetic variability and haplotypes of Echinococcus isolates from Tunisia[END_REF][START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF][START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF]Microsatellite Investigations of Multiple Echinococcus Granulosus Sensu Stricto Cysts in Single Hosts Reveal Different Patterns of Infection Events between Livestock and Humans[END_REF][START_REF] Oudni-M'rad | First molecular evidence of the simultaneous human infection with two species of Echinococcus granulosus sensu lato: Echinococcus granulosus sensu stricto and Echinococcus canadensis[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]).

In our study, we were able to genotype 44 E. granulosus s.l. isolates collected from humans living in western Algeria. Previous studies have shown that whatever the country or the host mitochondrial targets offer a high power of discrimination in regards to nuclear targets [START_REF] Laurimae | Genetic diversity and phylogeography of highly zoonotic Echinococcus granulosus genotype G1 in the Americas (Argentina, Brazil, Chile and Mexico) based on 8279bp of mtDNA[END_REF][START_REF] Lavikainen | Molecular characterization of Echinococcus isolates of cervid origin from Finland and Sweden[END_REF][START_REF] Maillard | Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries[END_REF]). We used a multilocus sequence typing scheme based on 4 fragments encoding mitochondrial genes with 1,626 nucleotides analyzed. This allowed the description of 19 haplotypes of which12 had never been reported, with 13 alleles newly described in Algeria of which 8 had not been previously deposited in GenBank. E. granulosus s.s. G1 genotype was the unique genotype identified for the all isolates tested in this study. This is in accordance with previous studies conducted in Algeria that found a frequency of 90.7 to 100% of this genotype in CE cases (Bardonnet et al. 2003;[START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]. This also agrees with the worldwide predominance of E. granulosus s.s. that would cause 88.44% of the human CE cases (Alvarez [START_REF] Rojas | Echinococcus granulosus sensu lato genotypes infecting humans--review of current knowledge[END_REF]. Surveys conducted in Tunisia and Morocco, two neighboring countries, also confirm that G1 genotype is predominant as causing human CE in North Africa [START_REF]Molecular evidence of ovine (G1) and camel (G6) strains of Echinococcus granulosus in Tunisia and putative role of cattle in human contamination[END_REF][START_REF] Oudni-M'rad | First molecular evidence of the simultaneous human infection with two species of Echinococcus granulosus sensu lato: Echinococcus granulosus sensu stricto and Echinococcus canadensis[END_REF][START_REF] Tahiri | Genotyping of human Echinococcus granulosus cyst in Morocco[END_REF]). However, while not detected in our study, it should be noted that both E. granulosus s.s. (G3) and E. canadensis (G6) have already been detected in Algeria [START_REF] Maillard | Taxonomic position and geographical distribution of the common sheep G1 and camel G6 strains of Echinococcus granulosus in three African countries[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF], the latter being mostly found in southern parts of Algeria where camelid breeding is common. These results are in accordance with the predominance of the G1 genotype in North Africa, warranting further studies to better understand the circulation of this species between the various hosts Molecular epidemiology surveys having analyzed the genetic diversity of E. granulosus s.l. diversity in Algeria remain rather rare. Zait et al. using a two-loci molecular system (cox1b and nad1) identified twenty different haplotypes among the 70 isolates tested, mostly originating from the Eastern part of Algeria, with a predominant one aggregating 71.6% of the isolates being identical to the reference mitogenome [START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]). More recently, Laatamna et al, used the full-length sequence of the cox1 gene to demonstrate a particularly high genetic diversity (73 different haplotypes among 125 isolates tested) in E. granulosus from livestock animals from the Djelfa province [START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF]. However, they also concluded on the identity between the predominant haplotype and the reference mitogenome.

To enhance our knowledge on the genetic diversity of E. granulosus s.s. in Algeria, we compared our data with previously published sequences. Comparison was limited due to different selections of genetic targets and the length of sequences analyzed. Nevertheless, we were able to compared the haplotype of 92 isolates collected from different regions of Algeria using a part of the cox1gene (locus cox1b of our study). Indeed, partial or complete sequence of the cox1 gene has been the most commonly used target for E. granulosus s.l. genotyping studies. Using this locus, we confirm the predominance of the cox1a_01allele, synonymous to the EG01 genotype, previously shown to cause most of human and animal CE cases in Algeria [START_REF] Laatamna | Frequency and genetic diversity of Echinococcus granulosus sensu stricto in sheep and cattle from the steppe region of Djelfa, Algeria[END_REF][START_REF] Zait | Molecular characterization of Echinococcus granulosus sensu stricto and Echinococcus canadensis in humans and livestock from Algeria[END_REF]. No segregation between isolates collected from humans or animals was noted supporting the integration of both hosts in the life cycle of the parasite.

Similarly, Algerian isolates of the G1 genotype irrespective of their geographic origin, shared a predominant haplotype or closely-related haplotypes, supporting the clonal expansion of the parasite throughout the country without host barrier, with further diversification (satellite haplotypes with limited genetic variation). This is in accordance with the mode of reproduction of the parasite that undergoes a sexual reproduction from a single worm thanks to a hermaphrodite genital apparatus.

However, using the 4 loci scheme, we were able to detect a substantially higher level of genetic diversity within the G1 genotype than using a single locus. All the haplotypes detected in our study were genetically close to but different from the G1reference mitogenome available in GenBank (AB786664) that has been isolated from a man in China [START_REF] Nakao | Mitochondrial phylogeny of the genus Echinococcus (Cestoda: Taeniidae) with emphasis on relationships among Echinococcus canadensis genotypes[END_REF]. As previous studies conducted in other parts of Algeria, we showed that the Hap01 haplotype is predominant in western Algeria. This synonymous nucleotide mutation, in a locus rarely included in the typing method, has already been described in Italian, Australian, Tunisian and Algerian isolates [START_REF] Kinkar | Long-read sequencing reveals a 4.4 kb tandem repeat region in the mitogenome of Echinococcus granulosus (sensu stricto) genotype G1[END_REF][START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF][START_REF] Sgroi | Cystic echinococcosis in wild boars (Sus scrofa) from southern Italy: Epidemiological survey and molecular characterization[END_REF]. The Hap01 haplotype belongs to a clonal complex that includes a low level of diversity with satellite haplotypes (9 haplotypes diverge only by one single nucleotide mutation). However, the second most frequent haplotype Hap02, that derives from Hap01, seems to form a new complex that gives birth to new closely related haplotypes. Whether this is due to the natural evolution of the species or the introduction of either cattle or sheep, or dogs from other regions should be further evaluated. The contamination of humans in other regions can also be hypothesized.

Interestingly, this haplotype has already been described from Kenchela, located in eastern Algeria. Similarly, Hap04 was shared by two isolates from Boumerdes and Laghouat, 2 cities distant from western Algeria. More recently, whole mitochondrial genome sequence using primer walking has been proposed for E. granulosus s.l. typing and offers a better discriminatory power and capability to analyze phylogenetic relationship). So, Kinkar et al. showed that Algerian isolates of E. granulosus s.l. are split into different geographical clusters that also include European and North African isolates [START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF]. This and results from other studies [START_REF] Boufana | Genetic variability and haplotypes of Echinococcus isolates from Tunisia[END_REF][START_REF] Hassan | Two haplotype clusters of Echinococcus granulosus sensu stricto in northern Iraq (Kurdistan region) support the hypothesis of a parasite cradle in the Middle East[END_REF][START_REF] Kinkar | Global phylogeography and genetic diversity of the zoonotic tapeworm Echinococcus granulosus sensu stricto genotype G1[END_REF], notably showing the low fixation indices between human and animal isolates, strongly suggest that genotype G1 population genetics has been shaped by intensive animal trade.

While the results of the present study are based on a relatively low number of isolates, they highlight the particularly high genetic diversity of E. granulosus s.s. in Algeria, with some specific features. To improve our knowledge and better understand how the parasite spread into this country and elsewhere, a consensus typing method should be defined allowing to aggregate together the data from offering the opportunity to conduct robust phylogeography analysis. This would be further applied to type both human and animal E. granulosus s.s.

Reference T G C C T T C T A T G T A C A T apt6_01 G apt6_02 T G apt6_03 C G apt6_04 G T apt6_05 T T G apt6_06 T G T apt6_07 A G apt6_08 C G apt6_09* T G apt6_10* G G apt6_11* T G C apt6_12* C G apt6_13* C G A C C nd3
Reference G A C T A G C A A A T T G A C cox1a_01 cox1a_02 G cox1a_03 G cox1a_04 A cox1a_05 G cox1a_06 T G cox1a_07 C cox1a_08 C cox1a_09 T cox1a_10 T cox1a_11* G C G cox1a_12* A cox1a_13* A cox1b 9822 9830 9853 9863 9870 9908 10054 10073 Reference A G C C T C T A cox1b_01 cox1b_02 T cox1b_03 T cox1b_04 T G cox1b_05 C cox1b_06 G cox1b_07* A T C 381 382

Table 1 :

 1 Sequence variability of 4 mitochondria loci observed in this study

	isolates

Table 2 :

 2 Polymorphic sites of the 4mitochondrial loci used in this study.

	Polymorphism in comparison with the reference mitochondrial genome (genotype G1, GenBank accession number AB786664) are indicated in
	Bold
	*Denotes sequences retrieved in GenBank

Table 3 :

 3 Allelic profiles of each haplotype *denotes haplotypes found in Genbank Fig.1. Minimum spanning tree of the cox1b locus drawn using the sequences obtained in this study and 98sequences from E. granulosus s.s. isolated from Algeria retrieved from GenBank. Minimum spanning tree of the concatenated haplotypes (atp6, nd3, cox1a, cox1b) from this study (dark blue) and 12 sequences from E. granulosus s.s. isolated from Algeria retrieved from GenBank (clear blue).

	1a: classification according to the host either human or animal; 1b: classification according to
	the geographical origin
	Circles represent sequence type; the distance between circles represents the number of
	mutations; circle diameter represents number of specimens with the corresponding sequence
	type.
	Accession numbers of sequences from GenBank used in this figure: AF408686.1,

Table S2 :

 S2 Primers used for amplification and sequencing of E. granulosus s.l. mitochondrial targets. Position on the complete reference mitochondrial genome (Genbank accession number AB786664)

	Figure S2
	5767..6279	8571..8918	9054..10727
	ATP6	NAD3	COX1
	atp6	nd3
	5661-6430	cox1a	cox1b
		8407-8956
		8878-9348	9762-10205

1

The authors declare that no funding was obtained for this study

The authors declare to have nothing to disclose All the data and remaining materials are available to the scientific community DM collected the samples, performed all the experiments and writes a first draft of the paper. KS supervise the biological diagnosis and review the paper. NM, ML, NB and BT took care of the patients and review the paper. CH supervised the experiments, analyzed the data and writes the paper Acknowledgements This study was supported by the Parasitology laboratory of the University of Oran1 Ahmed Ben Bella, the Department of Parasitology at the Hospital of Oran (EHU). The authors would like to thank Chafika Tachema for referring the specimens. The authors also thank the Joint Laboratory of Genetics and Molecular Biology and Sandra Vellaissamy from the Parasitology Department of St Antoine Hospital for excellent technical assistance.

Ethics statement

All the sequences were obtained from cysts collected from humans and no apparent geographic segregation trend was observed between these haplotypes.

Conflict of interest

The authors state that they have no conflict of interest. Supplementary data

Eg Algeria

This study


Noadya Monnier

Catherine Sarazin

Sonia Rippa
email: sonia.rippa@utc.fr

Transcriptomic dataset from Arabidopsis thaliana seedlings in response to Pseudomonas aeruginosa mono-rhamnolipids

Keywords: Rhamnolipids Arabidopsis Microarray Elicitor Biocontrol Plant defense Plant protection Visualization, Formal analysis, Data curation, Writing -original draft, Writing -review & editing; Catherine Sarazin: Conceptualization, Supervision, Writing -original draft, Writing -review Conceptualization, Visualization, Formal analysis

a b s t r a c t

The present data profile the large scale transcriptome changes in Arabidopsis thaliana Col-0 seedlings exposed to mono-rhamnolipids (Mono-RLs) from Pseudomonas aeruginosa secretome. Bacterial rhamnolipids (RLs) are biosurfactant known to trigger plant defense mechanisms and have a great potential for crop culture protection as environmentalfriendly biocontrol solution. They are thought to interact directly with membrane lipids to induce plant defense gene expression and protection towards phytopathogens. However, to date, data on the global transcriptomic modifications induced by these natural amphiphilic glycolipids in plants are missing. Ten-day-old seedlings were treated for 1 or 3 h with 100 μM Mono-RLs in liquid growth medium for root absorption. Total RNA samples were extracted, purified, labelled and hybridized to Agilent V4 Gene Expression Microarrays 4 × 44 K (design ID 021169) carrying 43803 ssDNA probes of 60-mer covering the entire genome of A. thaliana . The dataset was validated by quality assessments including RNA sample quality, microarray quality and global gene expression profiling. The raw and normalized formats of these transcriptomic data are available via GEO repository with the accession number GSE168830. The dataset can be used to provide insights into the plant's early and later mechanisms induced or repressed by RLs. It can be compared to data obtained with other plant defense elicitors, including the well described compounds perceived by membrane protein receptors.

© 2021 The Author(s). Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license ( http://creativecommons.org/licenses/by-nc-nd/4.0/ )

Specifications

Value of the Data

• The data provide Arabidopsis seedling transcriptomic changes that occur after short or longer exposure to mono-RLs. • The data can be used by the scientific community studying RL effects on plants and more largely plant defense triggering compounds. They can also be used by the phytosanitary industry developing biocontrol products based on RLs. • The data can be used as a resource to identify early or later genes differentially expressed after a rhamnolipid treatment and to identify marker genes to follow the RL defense triggering activity in plants.

• The data can be used to decipher the way of perception of amphiphilic compounds with plant defense triggering activity as well as affinity for plasma membrane lipids and to compare them with other plant defense elicitors.

Data Description

This dataset represents a large scale transcriptome comparison of Arabidopsis seedlings not exposed or exposed to Mono-RLs for 1 h or 3 h. Total RNA samples were extracted from the seedling tissues and were subjected to the microarray experiments using Agilent Arabidopsis V4 Gene Expression Microarrays (Agilent Technologies, Santa Clara, CA, USA). The flowchart of the experimental design of the study is presented ( Fig. 1 ). The raw and normalized formats of these data are available in National Center for Biotechnology information (NCBI) Gene Expression Omnibus (GEO) gene expression data repository ( https://www.ncbi.nlm.nih.gov/geo/query/ acc.cgi?acc=GSE168830 ). The data obtained after each processing step are provided as supplementary data files. Quality Control (QC) reports generated after array scanning and data extraction are provided in Supplemental Appendix S1. Final linear fit output values generated on the R software are gathered in Table 1. Expression value matrix after background correction, normalization and without probe replicates are supplied in Table 2. Unfiltered fold change data are gathered in Table 3. Reproducibility of the transcriptomic data from 5 independent replicates of each sample was confirmed by a principal component analysis (PCA) ( Fig. 2 ). The magnitude of the transcriptomic modulations was globally assessed with the dispersion of Fold Changes (FC) (Fig. 3) and Venn diagrams of significantly regulated transcripts ( Fig. 4 ).

Experimental Design, Materials and Methods

Mono-RLs solution preparation

Mono-RLs (mainly composed of α-L-rhamnopyranosyl-β-hydroxydecanoyl-β-hydroxydecanoate) were isolated from a commercial mixture (Jeneil Biotech, Inc, Saukville, USA). They were kindly provided by Dr Stéphan Dorey (RIBP, URCA, Reims, France). They were purified by the ICMR (URCA, Reims, France) by fast centrifugal partition chromatography (FCPC, Kromaton Technologies apparatus (Angers, France)) as previously described in [START_REF] Varnier | Bacterial rhamnolipids are novel MAMPs conferring resistance to Botrytis cinerea in grapevine[END_REF] . Mono-RLs initial stock was prepared in absolute ethanol at 20 mM concentration. To ensure complete dilution, this stock was diluted in water at 2 mM concentration (10% ethanol) [START_REF] Monnier | Rhamnolipids from Pseudomonas aeruginosa are elicitors triggering Brassica napus protection against Botrytis cinerea without physiological disorders[END_REF] .

Plant growth and treatment

A. thaliana genotype Col-0 corresponding to Nottingham Arabidopsis Stock Center (NASC) reference N1092 was used. The whole protocol was realized in sterile conditions and independently repeated 5 times, to collect 5 independent biological replicates. Seeds were sterilized for 5 min in 70% ethanol and 15 min in bleach (2.5% chloride) before being extensively rinsed with sterile water. They were then placed in petri dishes containing Murashige and Skoog [START_REF] Murashige | A revised medium for rapid growth and bio assays with tobacco tissue cultures[END_REF] (MS) solid medium (4.3 g L -1 MS (ref M5524), 0.5 g L -1 4-Morpholineethanesulfonic acid (MES), 5 g L -1 sucrose, 7 g L -1 agarose, all from Sigma Aldrich, Saint-Louis, USA), pH 5.7 (adjusted with KOH). Petri dishes were then placed for 4 days at 4 °C in the dark. For germination, seeds were placed in a climatic chamber at 21 °C, 60% relative humidity, 150 μmol m -2 s -1 light intensity with a 12-h photoperiod. After 4 days, 50 selected plants with similar development were divided in 5 groups of 10 plants, each one being placed in 1 mL of liquid MS medium (4.3 g L -1 MS, 0.5 g L -1 MES, 5 g L -1 sucrose). After 5 supplementary days into the climatic chamber, the growth medium of each group was replaced by 950 μL of fresh liquid MS medium. Treatments were realized 24 h after, by adding 50 μL of a solution containing 10% of ethanol (control) or 2 mM Mono-RLs (in 10 % ethanol) to culture medium in order to reach a final concentration of 0.5% ethanol (control) or 100 μM Mono-RLs (in 0.5% ethanol). Treatments were performed starting with the 3 h treatment in order to collect all samples at the same time (the 1 h treatment started 2 h later than the 3 h treatment). Seedlings were delicately harvested with a clamp, dried on filter paper, immediately frozen in liquid nitrogen and stored at -80 °C until RNA extraction. Five independent replicates were carried out with 10 seedlings.

Total RNA extraction, cRNA preparation and purity analysis

For each condition and each replicate, the 10 seedlings harvested were crushed together with mortar and pestle. RNA extractions were then conducted with the RNeasy Plant mini kit (Qiagen, Hilden, Germany, Ref 74904) according to provider specifications, including the DNA digestion step with the RNase free DNase set (Qiagen, Ref 79254,). RNA concentration and purity were determined using Thermo Fisher (Waltham, USA) Scientific Nanodrop 20 0 0. RNA integrity was checked using Bio-Rad (Hercules, USA) Experion TM and the corresponding kit Experion RNA StdSens Analysis (Bio-Rad, Ref 7007103) according to provider specifications. The gene expression study was realised using 100 ng RNA for each sample. The whole process was realized according to the Agilent protocol One-color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labelling and the Agilent equipment (Agilent Technologies, Santa Clara, CA, USA). First, spike-in was added to RNA (Spike-In-One-Color, Agilent, Ref 5188-5282). cDNA were then synthetized and used as template for labelled and amplified cRNA using the Low Input Quick Amp Labelling Kit One-Color (Agilent, Ref 5190-2305). cRNA were then purified using the RNeasy Plant Mini Kit (Qiagen, Ref 74904). Purified cRNA were analyzed with a Nanometer 20 0 0 (Thermo Fisher Scientific, Whaltam, USA). RNA integrity was validated by Experion TM chips. Purity (DO 260/DO 280 ≥2; 260/230 ≥2), yields ( ≥1.65 ng μL x 10 -3 elution volume in μL) and specific activities ( ≥6 pmol Cy3 / μg RNA) were checked.

Microarray hybridization

The microarrays used were V4 Gene Expression Microarray, 4 × 44 K, (4 repeats of 43803 ss-DNA probes of 60-mer covering all genome of A. thaliana , Agilent design ID 021169). cRNA were hybridized for 17 h on microarrays using the Gene Expression Hybridization Kit (Agilent, Ref 5188-5327) in the Shel Lab Agilent Microarray Hybridization Oven at 65 °C (ref G2545A, rotating system Ref G2530-6029). Hybridization chambers (ref G2534A) and Hybridization chambers gasket slides (Ref G2534-60011) were used. Deposits were organized by crossing biological independent experiences. The 5 repetitions on 7 arrays were hybridized in two times in order to minimize hybridizations. Slides were then washed 3 times with the Gene Expression Wash Buffer Kit (Agilent, ref 5188-5327).

Data acquisition and analysis

The arrays were immediately scanned with the SureScan Microarray Scanner (Agilent). The data extraction was performed with the Agilent software Feature Extraction version 11.5.1.1 using the default settings [START_REF] Agilent | agilent feature extraction[END_REF] . Quality Control (QC) reports generated showed that all evaluated metrics matched defined criteria. Processing of the dataset was realized using LIMMA (Linear Models for Microarray and RNA-Seq Data) package version 3.40.6 [START_REF] Ritchie | limma powers differential expression analyses for RNA-sequencing and microarray studies[END_REF] of the bioconductor project [START_REF] Huber | Orchestrating high-throughput genomic analysis with Bioconductor[END_REF] on R software version 3.6.1 [START_REF]R core TeamR: A Language and Environment for Statistical Computing[END_REF] . The different steps were made following LIMMA user's guide [START_REF] Smyth | Linear models for microarray data user' s guide[END_REF] and in particular with the single-channel case study on Agilent arrays. Briefly, a background correction was realized before a quantile normalization between arrays using respectively the « backgroundCorrect » and «normalizeBetweenArrays» functions. Control probes and probes above background on less than five arrays were filtered out. No more transformation was done on data transmitted to GEO NCBI (except removing replicates as requested). To validate the experimental process, a principal component analysis was realized using the PCA function of FactorMineR package version 2.4 [START_REF] Husson | Exploratory Multivariate Analysis by Example Using R[END_REF] . It confirmed three distinct groups of values corresponding to the control condition, the 1 h Mono-RL treatment and the 3 h Mono-RL treatment. Boxplots were generated with log(FC) values and were well centered on 0. Venn diagrams were realized, first considering probes with a corresponding p-value < 0.01 and with probes for which the condition |log(FC)| > 1 is also respected.

Fig. 1 .

 1 Fig. 1. Flowchart of experimental design of the study.

Fig. 2 .

 2 Fig. 2. PCA (principal component analysis) of the data from the different conditions.

Fig. 3 .

 3 Fig. 3. Dispersion of all log(FC) (Fold Changes) obtained from seedlings treated by Mono-RLs 1h or 3h compared to the control conditions.

Fig. 4 .

 4 Fig. 4. (A) Venn diagrams of significantly regulated transcripts ( p -value < 0.01). (B) Venn diagrams of regulated transcripts with a |log(FC)| > 1 and p -value < 0.01. Orange color: up-regulated, green color: down-regulated transcripts. (For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article.)

Table

	Subject	Biology
	Specific subject area	Transcriptomics of plants elicited by rhamnolipids
	Type of data	Raw data in .txt files
		Data table in Excel files (QC reports, expression value matrix, LIMMA
		output, Fold change data)
		Figures
	How data were acquired	Agilent Arabidopsis V4 Gene Expression Microarrays
	Data format	Raw and normalized data
	Parameters for data collection	5 samples of ten 10-day-old Col-0 Arabidopsis seedlings were
		transferred in liquid growth medium containing 0.5% EtOH (as control)
		or 100 μM Mono-RLs diluted in 0.5% EtOH (as Mono-RLs treated). They
		were harvested at 0, 1 and 3 h for total RNA extraction. cRNA were
		labelled and randomly hybridized on microarrays.
	Description of data collection	Background correction, quantile normalization and filtering were
		realized as described in the materials and methods section.
	Data source location	Université de Technologie de Compiègne, Compiègne, France

Acknowledgments

We thank Dr Stéphan Dorey (Résistance Induite et Bioprotection des Plantes laboratory, Université Reims Champagne-Ardenne) for having provided us Mono-RLs purified by the Institut de Chimie Moléculaire de Reims. This research was supported by the Hauts-de-France (HdF) Council and European Regional Development Fund (ERDF), and was realized in the context of the

Data accessibility Normalized and raw data are available in Gene Expression Omnibus (GEO) database of NCBI with accession number GSE168830 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE168830 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171040 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171041 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171042 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171043 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171044 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171045 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171046 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171047 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171048 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171049 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171050 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171051 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171052 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171053 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171054 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171055 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171056 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171057 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171058 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171059 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171060 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171061 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171062 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171063 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM5171064

Ethics Statement

No animal or human experiments were performed to obtain the data.

Declaration of Competing Interest

The authors declare that they have no known competing financial interests or personal relationships which have or could be perceived to have influenced the work reported in this article.

MAELIA project. N.M. Ph.D. thesis was co-funded by HdF Council and ERDF. HdF Council and ERDF also co-founded equipment utilized within CPER 2007-2020.

Supplementary Materials

Supplementary material associated with this article can be found in the online version at doi: 10.1016/j.dib.2021.107397 .