A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics

Abstract

cabbage (Brassica oleracea var. capitata) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and health-promoting substances. To facilitate further genetics and genomic studies and crop improvement, we present here a high-quality reference genome for cabbage. We report a de novo genome assembly of the cabbage double-haploid line D134. A combined strategy of single-molecule real-time (SMRT) sequencing, 10× Genomics and chromosome conformation capture (Hi-c) produced a high quality cabbage draft genome. the chromosome-level D134 assembly is 529.92 Mb in size, 135 Mb longer than the current 02-12 reference genome, with scaffold N50 length being raised as high as 38 times. We annotated 44,701 high-quality protein-coding genes, and provided full-length transcripts for 45.59% of the total predicted gene models. Moreover, we identified novel genomic features like underrated TEs, as well as gene families and gene family expansions and contractions during B. oleracea evolution. The D134 draft genome is a cabbage reference genome assembled by SMRT long-read sequencing combined with the 10× Genomics and Hi-C technologies for scaffolding. This high-quality cabbage reference genome provides a valuable tool for improvement of Brassica crops. Brassica oleracea is an important vegetable species widely grown throughout the world. The species comprises several subspecies showing extensive morphological and phytochemical diversity. As a diploid species, B. oleracea underwent a whole-genome triplication (WGT) event 1 , followed by two whole-genome duplication (WGD) event 2,3 and a specific WGT 4 of the Brassiceae lineage, thus becoming a model for studies on polyploid genome evolution. Currently, two B. oleracea genomes based on next-generation sequencing (NGS) technology are available: the TO1000 (kale-like; B. oleracea var. alboglabra) assembly and the 02-12 (cabbage; B. oleracea var. capitata) assembly 5,6 , but their errors and gaps make them difficult to use for many studies 7-10. Recently, B. oleracea L. var. italica (broccoli) genome assembly was completed using long reads and optical maps 11. Broccoli and cabbage belong to Brassica species, however their growth, morphology and molecular levels is extremely variable, showing the importance of generating several genome assemblies for different morphotypes of B. oleracea. Up to now, there is still no high quality, comprehensive assembled cabbage (B. oleracea var. capitata) genome, which hinders greatly basic genetics and genomics research, as well as crop improvement. Thus generating an accurate cabbage genome assembly is crucial. To obtain a homozygous genome, the cabbage double-haploid (DH) line D134 was produced by microspore culture. We conducted whole-genome sequencing and de novo assembly for this line using single-molecule realtime (SMRT) cells on a PacBio Sequel platform combined with high-throughput chromosome conformation capture (Hi-C), next generation sequencing (NGS) and 10× Genomics technologies. This genome assembly is...

Long-read assembly of the Brassica napus reference genome Darmor-bzh

“…The first 2, B. rapa Z1 and B. oleracea HDEM, were published in 2018 and generated using ONT reads and optical maps [ 2 , 4 ]. At the beginning of 2020, 2 genomes of B. rapa (Chiifu) and B. oleracea (D134) were released and sequenced using PacBio long reads [ 5 , 6 ]. A first long-read assembly based on ONT of the other diploid species, B. nigra NI100, has been available since the beginning of 2020 [ 7 ].…”

Genome-Wide Analysis of Simple Sequence Repeats in Cabbage (Brassica oleracea L.)

“…The release of reference genome of cabbage has produced numerous sequences, which are adopted to develop and identify cabbage SSR markers ( Cai et al, 2020 ; Lv et al, 2020 ). Thus, the present work focused on identifying SSRs at genome-wide level in the cabbage line TO1000, a homozygous doubled haploid, and evaluate them for marker development.…”

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

“…The Brassica database, BRAD 1 , provides the information on the genome assemblies, predicted gene models, and gene annotations of 25 Brassica species ( Cheng et al, 2011 ), helping plant scientists and breeders to efficiently use the information to understand the complex mechanisms underlying disease resistance. The molecular aspects of B. oleracea –pathogen interactions could be revealed by using high-quality reference genome assemblies generated for different morphotypes of B. oleracea over the past several years including kale ( Parkin et al, 2014 ), cabbage ( Cai et al, 2020 ; Lv et al, 2020 ; Guo et al, 2021 ), cauliflower ( Sun et al, 2019 ; Guo et al, 2021 ), and broccoli ( Belser et al, 2018 ). But the high-quality genome assemblies of the reference genome of B. oleracea may not represent all the morphotypes and capture only a fraction of them such as inflorescence in ‘C-8’ ( Sun et al, 2019 ) and leafy type in ‘TO1000’ ( Parkin et al, 2014 ) leaving other morphotypes, such as lateral leaf buds (brussels sprouts) and tuberous stems (kohlrabi) not having genome assemblies.…”