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.
Highlights
Brassica oleracea is an important vegetable species widely grown throughout the world
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), generation sequencing (NGS) and 10× Genomics technologies
A set of DH cabbage lines were previously obtained from a cross of the two cabbage inbred lines 96–100 and 01–20 using microspore culture, and this DH population has been extensively used in recent years to successfully mapped a series of important agronomic trait genes/QTLs for cabbage, including Fusarium wilt resistance, head weight, plant height, maturing period and seed number[12,13,14,15,16]
Summary
Brassica oleracea is an important vegetable species widely grown throughout the world. Broccoli and cabbage belong to Brassica species, their growth, morphology and molecular levels is extremely variable, showing the importance of generating several genome assemblies for different morphotypes of B. oleracea. There is still no high quality, comprehensive assembled cabbage 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), generation sequencing (NGS) and 10× Genomics technologies. This genome assembly is a draft genome for cabbage by Third-Generation Sequencing
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