Abstract
Rapeseed (Brassica napus), the second most important oilseed crop globally, originated from an interspecific hybridization between B. rapa and B. oleracea. After this genome collision, B. napus underwent extensive genome restructuring, via homoeologous chromosome exchanges, resulting in widespread segmental deletions and duplications. Illicit pairing among genetically similar homoeologous chromosomes during meiosis is common in recent allopolyploids like B. napus, and post-polyploidization restructuring compounds the difficulties of assembling a complex polyploid plant genome. Specifically, genomic rearrangements between highly similar chromosomes are challenging to detect due to the limitation of sequencing read length and ambiguous alignment of reads. Recent advances in long read sequencing technologies provide promising new opportunities to unravel the genome complexities of B. napus by encompassing breakpoints of genomic rearrangements with high specificity. Moreover, recent evidence revealed ongoing genomic exchanges in natural B. napus, highlighting the need for multiple reference genomes to capture structural variants between accessions. Here we report the first long-read genome assembly of a winter B. napus cultivar. We sequenced the German winter oilseed rape accession ‘Express 617’ using 54.5x of long reads. Short reads, linked reads, optical map data and high-density genetic maps were used to further correct and scaffold the assembly to form pseudochromosomes. The assembled Express 617 genome provides another valuable resource for Brassica genomics in understanding the genetic consequences of polyploidization, crop domestication, and breeding of recently-formed crop species.
Highlights
Brassica napus subsp. oleifera, commonly known as rapeseed or canola, is the second most important oilseed crop globally (Food and Agriculture Organization of the United Nations, 2019)
Improved contiguity of Express 617 genome in comparison to other B. napus assemblies is evident in the low number of scaffolds, high N50 scaffold length and the low percentage of Ns in total genome size (Table 1)
ZS11 and Darmor-bzh were constructed with more comprehensive data, including higher coverage of short read sequencing, long range mate-paired reads and BAC-by-BAC approach (Sanger-sequenced for Darmor-bzh and Illumina-sequenced for ZS11) (Chalhoub et al, 2014; Sun et al, 2017)
Summary
Brassica napus subsp. oleifera, commonly known as rapeseed or canola, is the second most important oilseed crop globally (Food and Agriculture Organization of the United Nations, 2019). The mixture of older, fixed HEs and newly-formed HEs explains the wide-spread variations, such as reciprocal (Lombard and Delourme, 2001; Osborn et al, 2003; Piquemal et al, 2005) and non-reciprocal (Udall et al, 2005) translocations, between genotypes These genotype-specific HEs have been shown to give rise to novel genetic diversities related to important agronomic traits such as flowering time (Pires et al, 2004; Chalhoub et al, 2014; Schiessl et al, 2017), leaf morphology (Osborn et al, 2003; Gaeta et al, 2007), and seed content (Harper et al, 2012; Qian et al, 2016)
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Free) 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
