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

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 ca...

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Published in	Scientific reports Vol. 10; no. 1; p. 12394
Main Authors	Lv, Honghao, Wang, Yong, Han, Fengqing, Ji, Jialei, Fang, Zhiyuan, Zhuang, Mu, Li, Zhansheng, Zhang, Yangyong, Yang, Limei
Format	Journal Article
Language	English
Published	London Nature Publishing Group UK 24.07.2020 Nature Publishing Group
Subjects	631/208/212 631/449 Brassica - genetics Brassica oleracea Crop improvement Evolution, Molecular Gene families Genetics Genomes Genomics Genomics - standards Health promotion Humanities and Social Sciences Molecular Sequence Annotation multidisciplinary Nutrients Polymorphism, Single Nucleotide Quality Reference Standards Science Science (multidisciplinary) Sequence Analysis Single Molecule Imaging SMRT protein
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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.
AbstractList	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. 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. 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.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. 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.
ArticleNumber	12394
Author	Ji, Jialei Li, Zhansheng Zhuang, Mu Zhang, Yangyong Lv, Honghao Han, Fengqing Fang, Zhiyuan Yang, Limei Wang, Yong
Author_xml	– sequence: 1 givenname: Honghao surname: Lv fullname: Lv, Honghao organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 2 givenname: Yong surname: Wang fullname: Wang, Yong organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 3 givenname: Fengqing surname: Han fullname: Han, Fengqing organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 4 givenname: Jialei surname: Ji fullname: Ji, Jialei organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 5 givenname: Zhiyuan surname: Fang fullname: Fang, Zhiyuan organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 6 givenname: Mu surname: Zhuang fullname: Zhuang, Mu organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 7 givenname: Zhansheng surname: Li fullname: Li, Zhansheng organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 8 givenname: Yangyong surname: Zhang fullname: Zhang, Yangyong email: zhangyangyong@caas.cn organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture – sequence: 9 givenname: Limei surname: Yang fullname: Yang, Limei email: yanglimei@caas.cn organization: Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/32709963$$D View this record in MEDLINE/PubMed
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Snippet	Cabbage ( Brassica oleracea var. capitata ) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and... Cabbage (Brassica oleracea var. capitata) is an important vegetable crop widely grown throughout the world, providing plentiful nutrients and health-promoting...
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SubjectTerms	631/208/212 631/449 Brassica - genetics Brassica oleracea Crop improvement Evolution, Molecular Gene families Genetics Genomes Genomics Genomics - standards Health promotion Humanities and Social Sciences Molecular Sequence Annotation multidisciplinary Nutrients Polymorphism, Single Nucleotide Quality Reference Standards Science Science (multidisciplinary) Sequence Analysis Single Molecule Imaging SMRT protein
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Title	A high-quality reference genome for cabbage obtained with SMRT reveals novel genomic features and evolutionary characteristics
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