Deniot, G. | Search bioRxiv

bioRxiv2020

Long-reads assembly of the Brassica napus reference genome, Darmor-bzh

BackgroundThe combination of long-reads and long-range information to produce genome assemblies is now accepted as a common standard. This strategy not only allow to access the gene catalogue of a given species but also reveals the architecture and organisation of chromosomes, including complex regions like telomeres and centromeres. The Brassica genus is not exempt and many assemblies based on long reads are now available. The reference genome for Brassica napus, Darmor-bzh, which was published in 2014, has been produced using short-reads and its contiguity was extremely low if compared to current assemblies of the Brassica genus. FindingsHere, we report the new long-reads assembly of Darmor-bzh genome (Brassica napus) generated by combining long-reads sequencing data, optical and genetic maps. Using the PromethION device and six flowcells, we generated about 16M long-reads representing 93X coverage and more importantly 6X with reads longer than 100Kb. This ultralong-reads dataset allows us to generate one of the most contiguous and complete assembly of a Brassica genome to date (contigs N50 > 10Mb). In addition, we exploited all the advantages of the nanopore technology to detect modified bases and sequence transcriptomic data using direct RNA to annotate the genome and focus on resistance genes. ConclusionUsing these cutting edge technologies, and in particular by relying on all the advantages of the nanopore technology, we provide the most contiguous Brassica napus assembly, a resource that will be valuable for the Brassica community for crop improvement and will facilitate the rapid selection of agronomically important traits.

genomics↗

bioRxiv2020

Large genomic variants reveal unexplored intraspecific diversity in Brassica rapa genomes

ABSTRACTTraditionally, reference genomes in crop species rely on the assembly of one accession, thus occulting most of intraspecific diversity. However, rearrangements, gene duplications and transposable element content may have a large impact on the genomic structure, which could generate new phenotypic traits. Using two Brassica rapa genomes recently sequenced and assembled using long-read technology and optical mapping, we investigated structural variants and repetitive content between the two accessions and genome size variation among a core collection.We explored the structural consequences of the presence of large repeated sequences in B. rapa ‘Z1’ genome versus the B. rapa ‘Chiifu’ genome, using comparative genomics and cytogenetic approaches. First, we showed that large genomic variants on chromosomes A05, A06, A09 and A10 are due to large insertions and inversions when comparing B. rapa ‘Z1’ and B. rapa ‘Chiifu’ at the origin of important length differences in some chromosomes. For instance, lengths of ‘Z1’ and ‘Chiifu’ A06 chromosomes were estimated in silico to be 55Mb and 29Mb, respectively. To validate these observations, we compared using fluorescent in-situ hybridization (FISH) the two A06 chromosomes present in a F1 hybrid produced by crossing these two varieties. We confirmed a length difference of 17.6% between the A06 chromosomes of ‘Z1’ compared to ‘Chiifu’. Alternatively, using a Copy Number Variation approach, we were able to quantify the presence of a higher number of rDNA and Gypsy elements in ‘Z1’ genome compared to ‘Chiifu’ on different chromosomes including A06. Using flow cytometry, the total genome size of 12 Brassica accessions corresponding to a B. rapa available core collection was estimated and revealed a genome size variation of up to 16% between these accessions as well as some shared inversions.This study revealed the contribution of long-read sequencing of new accessions belonging to different cultigroups of B. rapa and highlighted the potential impact of differential insertion of repeat elements and inversions of large genomic regions in genome size intraspecific variability.Competing Interest StatementThe authors have declared no competing interest.View Full Text

genomics↗