A high‐quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance

Abstract

Summary Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high‐quality genome assembly of a typical semi‐winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single‐molecule sequencing and chromosome conformation capture (Hi‐C) techniques. Most of the high‐confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR‐RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide‐binding leucine‐rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head‐to‐head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi‐winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.

Modelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids

“…A recent high‐quality genome of B. napus cv. ZS11 (Chen et al ., 2021 ) found similar recent repeat expansions compared to the diploid ancestor which supports our findings.…”

The impacts of allopolyploidization on Methyl-CpG-Binding Domain (MBD) gene family in Brassica napus

“…B. napus may enhance its adaptability to the environment through the regulation of cis -acting elements. On the other hand, TE amplification may have driven the formation of the B. napus genome [ 54 ]. We identified 83, 88 and 182 TE fragments within 2000 bp upstream and downstream of the MBD gene in the B. rapa , B. oleracea and B. napus genomes, respectively.…”

Daisychain: Search and Interactive Visualisation of Homologs in Genome Assemblies

“…It is not possible for users to upload their own data but local instances of Daisychain with different datasets can be hosted using the code publicly available at https://github.com/AppliedBioinformatics/gene-daisychain under GNU Lesser General Public License v3. BnaA07g28760D [36], its 3′ and 5′ neighbors and other homologs in the B. napus v4.1 annotation [12] (grey circles), compared with the B. napus ZS11 annotation [16] (pink circle), the B. napus Tapidor annotation (orange circles) and the Darmor-bzh v8.1 annotation (blue circles) [14]. The B. napus v4.1 annotation contains 3 homologs for the candidate gene, while the ZS11 and Tapidor annotations both contain only one homolog.…”

“…One example is Brassica napus in plants. The first reference genome for B. napus was published in 2014 [12], followed by two other cultivars' genome assemblies in 2017 [13,14], then eight high-quality genomes in 2020 [15] and two high-quality versions of earlier published genomes in 2021 [16,17]. The number of available bacterial genomes has exploded; for Escherichia coli alone, there are now more than 10,000 available genome assemblies [18].…”

“…Figure 3. Visualisation of gene homologies with Daisychain-Web for the disease resistance gene Rlm1 candidate geneBnaA07g28760D[36], its 3′ and 5′ neighbors and other homologs in the B. napus v4.1 annotation[12] (grey circles), compared with the B. napus ZS11 annotation[16] (pink circle), the B. napus Tapidor annotation (orange circles) and the Darmor-bzh v8.1 annotation (blue circles)[14]. The B. napus v4.1 annotation contains 3 homologs for the candidate gene, while the ZS11 and Tapidor annotations both contain only one homolog.…”