Berline Fopa Fomeju

Aurélie Berard

Isabelle Le Clainche

Aurélie Canaguier

Elodie Belmonte

Veronique Gautier

Charles Poncet

Marie-Christine Le Paslier

Guillaume Frémondière

Damien Hinsinger

Long Reads for Long-Term Goals : A Genome Resource for Lavander Genetic Improvement

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Long Reads for Long-Term Goals : A Genome Resource for Lavender Genetic Improvement

Synteny with JingXu2 (JX)

• 54 Maillette contigs anchored on 27 chr. JX • 839 markers from 3,766 loci (NEBnext direct Genotyping Solution v2) • + 36 Maillette contigs anchored in 80 JX scaffolds (not shown)

• Contigs with telomere repeats (one end )  12 anchored on JX chr (green contigs in view)  24 anchored on scaffolds  6 without anchorage

Materials & methods

Young leaves from an individual of the cultivar 'Maillette' were collected and immediately flash frozen. The protocol 'Plant Leaves' (dx.doi.org/10.17504/protocols.io.bp2l694yzlqe/v1) was slightly modified and the obtained DNA medusa was used for long reads sequencing. A Pacbio HiFi library was built following the manufacturer's instructions, then sequenced on a Sequel II at Gentyane (INRAE, Clermont-Ferrand) and HiFi reads generated. Assembly was performed with HiFiAsm using default parameters. Assembly quality was assessed using BUSCO, Merqury and KAT. Repeated Sequences were identified with RepeatModeler/RepeatMasker. Synteny with the genome sequence of the cultivar JingXu2 was assessed by mapping context sequences from a panel designed at EPGV (INRAE, Evry) during the GenoLavande project on sequences from both assemblies, then assessing the markers showing a '1 to 1' relationship.

Perspectives

• Expand contigs with available Nanopore long reads (data not shown)

• Scaffolding to pseudomolecules with genetic map (currently under construction) • Gene and repeat annotations • Compare with scaffolding from Hi-C linked reads

The lavender genome is composed of 68.23% of repeated sequences (mainly Copia -36.13%).

this study) Maillette (Malli et al. 2019) JingXu2 (Li et al. 2021)

  Berline Fopa Fomeju 1 , Aurélie Berard 2 , Isabelle Le Clainche 2 , Aurélie Canaguier 2 , Elodie Belmonte 3 , Véronique Gautier 3 , Charles Poncet 3 , Marie-Christine Le Paslier 2 , Guillaume Frémondière 4 , Damien D. Hinsinger 2 and

	Patricia Faivre-Rampant 2
	1 ITEIPMAI, Chemille en Anjou, France
	2 INRAE, Evry, France
	3 INRAE, Clermont-Ferrand, France
	4 ITEIPMAI, Montboucher sur Jabron, France
	Metrics of Lavender assemblies
	Chromosome number		25	25	27
	Sequencing technologies	Pacbio HiFi	Illumina + transcriptome	PacBio CLC + 10X + Hi-C
	Estimate of genome size (Mb)		721.73	~850	1016.25
	Total length of contigs (Mb)		891.5	688.04	911.14
	Total number of contigs		579	1383
	N50 of contigs (Mb)			20.35	1.22
	Largest contig (bp)		35,738,470	9,968,313
	Total length of scaffolds (Mb)			869.79	914.49
	Total number of scaffolds			84,291	306
	N50 of scaffolds (Mb)			0.097	36.20
	Largest scaffold (Mb)				0.94	46.64
	GC content (%)			39.18	38.1	38.58
	Complete BUSCOs (%)		97.1	89.7	91.4
	Repeat density (%)			68.23	42.8	58.28
	Number of protein-coding genes		ongoing	62,141	65,905
	Assembly
	Quality BUSCO (eudicot_odb10,	C:97.1%[S:24.7%,D:72.4%],F:0.6%,M:2.3%
	n:2326)
	Merqury completeness 83.0479
					Conclusions
					• Assembly more contiguous
	Other	Results	-	(N50 of contigs) • Better completion
					• 839 markers used
	Cytology			to check collinearity
	Using chromosome counting and rDNA staining (realised at the Molecular Cytogenetics platform -INRAE Le Rheu),	 Synteny with JingXu2 (supported by several markers)  Hypothesis: JingXu2 chr4 and chr25 = one chromosome in Maillette (partially contig 28)
	we found 25 chromosomes, as
	well as 8 45S rDNA clusters, in
	'Maillette' root tip cells.
					Maillette (2n=50)

Merqury QV (error rate) 41.7636 (6.66247e-05)

Aknowledgements

Molecular Cytogenetics platform -INRAE Le Rheu

Associated publication : Genespace lavande : Fopa Fomeju B, Brunel D, Bérard A, Rivoal J-B, Gallois P, Le Paslier M-C, et al 2020 Quick and efficient approach to develop genomic resources in orphan species: Application in Lavandula angustifolia. PLoS ONE 15(12): e0243853. https://doi.org/10.1371/journal.pone.0243853 Maillette (