A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution
Chinese flowering cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality <i>de novo</i> assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chi...
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MDPI AG
2023-06-01
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| author | Guangguang Li Ding Jiang Juntao Wang Yi Liao Ting Zhang Hua Zhang Xiuchun Dai Hailong Ren Changming Chen Yansong Zheng |
| author_facet | Guangguang Li Ding Jiang Juntao Wang Yi Liao Ting Zhang Hua Zhang Xiuchun Dai Hailong Ren Changming Chen Yansong Zheng |
| author_sort | Guangguang Li |
| collection | DOAJ |
| description | Chinese flowering cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality <i>de novo</i> assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA transposons and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, <i>Brassica juncea</i>. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely driven by LTR-retrotransposon amplification. Furthermore, we identified a large number of structural variations (SVs) within the <i>B. rapa</i> lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of <i>B. rapa</i> crops. |
| first_indexed | 2024-03-11T01:31:51Z |
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| language | English |
| last_indexed | 2024-03-11T01:31:51Z |
| publishDate | 2023-06-01 |
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| record_format | Article |
| series | Plants |
| spelling | doaj.art-f6aa9d963d8547f3986a85faad0920df2023-11-18T17:18:20ZengMDPI AGPlants2223-77472023-06-011213249810.3390/plants12132498A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure EvolutionGuangguang Li0Ding Jiang1Juntao Wang2Yi Liao3Ting Zhang4Hua Zhang5Xiuchun Dai6Hailong Ren7Changming Chen8Yansong Zheng9Guangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaGuangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaCollege of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaCollege of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaCollege of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaGuangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaGuangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaGuangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaCollege of Horticulture, South China Agricultural University, Guangzhou 510642, ChinaGuangzhou Academy of Agricultural Sciences, Guangzhou 510335, ChinaChinese flowering cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) is a popular and widely cultivated leaf vegetable crop in Asia. Here, we performed a high quality <i>de novo</i> assembly of the 384 Mb genome of 10 chromosomes of a typical cultivar of Chinese flowering cabbage with an integrated approach using PacBio, Illumina, and Hi-C technology. We modeled 47,598 protein-coding genes in this analysis and annotated 52% (205.9/384) of its genome as repetitive sequences including 17% in DNA transposons and 22% in long terminal retrotransposons (LTRs). Phylogenetic analysis reveals the genome of the Chinese flowering cabbage has a closer evolutionary relationship with the AA diploid progenitor of the allotetraploid species, <i>Brassica juncea</i>. Comparative genomic analysis of Brassica species with different subgenome types (A, B and C) reveals that the pericentromeric regions on chromosome 5 and 6 of the AA genome have been significantly expanded compared to the orthologous genomic regions in the BB and CC genomes, largely driven by LTR-retrotransposon amplification. Furthermore, we identified a large number of structural variations (SVs) within the <i>B. rapa</i> lines that could impact coding genes, suggesting the functional significance of SVs on Brassica genome evolution. Overall, our high-quality genome assembly of the Chinese flowering cabbage provides a valuable genetic resource for deciphering the genome evolution of Brassica species and it can potentially serve as the reference genome guiding the molecular breeding practice of <i>B. rapa</i> crops.https://www.mdpi.com/2223-7747/12/13/2498Chinese flowering cabbage<i>Brassica rapa</i> var. <i>parachinensis</i>genome structure evolutionassemblyPacBioHi-C |
| spellingShingle | Guangguang Li Ding Jiang Juntao Wang Yi Liao Ting Zhang Hua Zhang Xiuchun Dai Hailong Ren Changming Chen Yansong Zheng A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution Plants Chinese flowering cabbage <i>Brassica rapa</i> var. <i>parachinensis</i> genome structure evolution assembly PacBio Hi-C |
| title | A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution |
| title_full | A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution |
| title_fullStr | A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution |
| title_full_unstemmed | A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution |
| title_short | A High-Continuity Genome Assembly of Chinese Flowering Cabbage (<i>Brassica rapa</i> var. <i>parachinensis</i>) Provides New Insights into Brassica Genome Structure Evolution |
| title_sort | high continuity genome assembly of chinese flowering cabbage i brassica rapa i var i parachinensis i provides new insights into brassica genome structure evolution |
| topic | Chinese flowering cabbage <i>Brassica rapa</i> var. <i>parachinensis</i> genome structure evolution assembly PacBio Hi-C |
| url | https://www.mdpi.com/2223-7747/12/13/2498 |
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