Cargando…
Reference genomes of the two cultivated jute species
Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each compr...
Autores principales: | , , , , , , , , , , , , , , , , , , , , , , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
John Wiley and Sons Inc.
2021
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541789/ https://www.ncbi.nlm.nih.gov/pubmed/34170619 http://dx.doi.org/10.1111/pbi.13652 |
_version_ | 1784589315319267328 |
---|---|
author | Zhang, Lilan Ma, Xiaokai Zhang, Xingtan Xu, Yi Ibrahim, Aminu Kurawa Yao, Jiayu Huang, Huaxing Chen, Shuai Liao, Zhenyang Zhang, Qing Niyitanga, Sylvain Yu, Jiaxin Liu, Yi Xu, Xiuming Wang, Jingjing Tao, Aifen Xu, Jiantang Chen, Siyuan Yang, Xin He, Qingyao Lin, Lihui Fang, Pingping Zhang, Liemei Ming, Ray Qi, Jianmin Zhang, Liwu |
author_facet | Zhang, Lilan Ma, Xiaokai Zhang, Xingtan Xu, Yi Ibrahim, Aminu Kurawa Yao, Jiayu Huang, Huaxing Chen, Shuai Liao, Zhenyang Zhang, Qing Niyitanga, Sylvain Yu, Jiaxin Liu, Yi Xu, Xiuming Wang, Jingjing Tao, Aifen Xu, Jiantang Chen, Siyuan Yang, Xin He, Qingyao Lin, Lihui Fang, Pingping Zhang, Liemei Ming, Ray Qi, Jianmin Zhang, Liwu |
author_sort | Zhang, Lilan |
collection | PubMed |
description | Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops. |
format | Online Article Text |
id | pubmed-8541789 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | John Wiley and Sons Inc. |
record_format | MEDLINE/PubMed |
spelling | pubmed-85417892021-10-29 Reference genomes of the two cultivated jute species Zhang, Lilan Ma, Xiaokai Zhang, Xingtan Xu, Yi Ibrahim, Aminu Kurawa Yao, Jiayu Huang, Huaxing Chen, Shuai Liao, Zhenyang Zhang, Qing Niyitanga, Sylvain Yu, Jiaxin Liu, Yi Xu, Xiuming Wang, Jingjing Tao, Aifen Xu, Jiantang Chen, Siyuan Yang, Xin He, Qingyao Lin, Lihui Fang, Pingping Zhang, Liemei Ming, Ray Qi, Jianmin Zhang, Liwu Plant Biotechnol J Research Articles Cultivated jute, which comprises the two species Corchorus capsularis and C. olitorius, is the second most important natural fibre source after cotton. Here we describe chromosome‐level assemblies of the genomes of both cultivated species. The C. capsularis and C. olitorius assemblies are each comprised of seven pseudo‐chromosomes, with the C. capsularis assembly consisting of 336 Mb with 25,874 genes and the C. olitorius assembly containing 361 Mb with 28 479 genes. Although the two Corchorus genomes exhibit collinearity, the genome of C. olitorius contains 25 Mb of additional sequences than that of C. capsularis with 13 putative inversions, which might give a hint to the difference of phenotypic variants between the two cultivated jute species. Analysis of gene expression in isolated fibre tissues reveals candidate genes involved in fibre development. Our analysis of the population structures of 242 cultivars from C. capsularis and 57 cultivars from C. olitorius by whole‐genome resequencing resulted in post‐domestication bottlenecks occurred ~2000 years ago in these species. We identified hundreds of putative significant marker‐trait associations (MTAs) controlling fibre fineness, cellulose content and lignin content of fibre by integrating data from genome‐wide association studies (GWAS) with data from analyses of selective sweeps due to natural and artificial selection in these two jute species. Among them, we further validated that CcCOBRA1 and CcC4H1 regulate fibre quality in transgenic plants via improving the biosynthesis of the secondary cell wall. Our results yielded important new resources for functional genomics research and genetic improvement in jute and allied fibre crops. John Wiley and Sons Inc. 2021-07-08 2021-11 /pmc/articles/PMC8541789/ /pubmed/34170619 http://dx.doi.org/10.1111/pbi.13652 Text en © 2021 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Articles Zhang, Lilan Ma, Xiaokai Zhang, Xingtan Xu, Yi Ibrahim, Aminu Kurawa Yao, Jiayu Huang, Huaxing Chen, Shuai Liao, Zhenyang Zhang, Qing Niyitanga, Sylvain Yu, Jiaxin Liu, Yi Xu, Xiuming Wang, Jingjing Tao, Aifen Xu, Jiantang Chen, Siyuan Yang, Xin He, Qingyao Lin, Lihui Fang, Pingping Zhang, Liemei Ming, Ray Qi, Jianmin Zhang, Liwu Reference genomes of the two cultivated jute species |
title | Reference genomes of the two cultivated jute species |
title_full | Reference genomes of the two cultivated jute species |
title_fullStr | Reference genomes of the two cultivated jute species |
title_full_unstemmed | Reference genomes of the two cultivated jute species |
title_short | Reference genomes of the two cultivated jute species |
title_sort | reference genomes of the two cultivated jute species |
topic | Research Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8541789/ https://www.ncbi.nlm.nih.gov/pubmed/34170619 http://dx.doi.org/10.1111/pbi.13652 |
work_keys_str_mv | AT zhanglilan referencegenomesofthetwocultivatedjutespecies AT maxiaokai referencegenomesofthetwocultivatedjutespecies AT zhangxingtan referencegenomesofthetwocultivatedjutespecies AT xuyi referencegenomesofthetwocultivatedjutespecies AT ibrahimaminukurawa referencegenomesofthetwocultivatedjutespecies AT yaojiayu referencegenomesofthetwocultivatedjutespecies AT huanghuaxing referencegenomesofthetwocultivatedjutespecies AT chenshuai referencegenomesofthetwocultivatedjutespecies AT liaozhenyang referencegenomesofthetwocultivatedjutespecies AT zhangqing referencegenomesofthetwocultivatedjutespecies AT niyitangasylvain referencegenomesofthetwocultivatedjutespecies AT yujiaxin referencegenomesofthetwocultivatedjutespecies AT liuyi referencegenomesofthetwocultivatedjutespecies AT xuxiuming referencegenomesofthetwocultivatedjutespecies AT wangjingjing referencegenomesofthetwocultivatedjutespecies AT taoaifen referencegenomesofthetwocultivatedjutespecies AT xujiantang referencegenomesofthetwocultivatedjutespecies AT chensiyuan referencegenomesofthetwocultivatedjutespecies AT yangxin referencegenomesofthetwocultivatedjutespecies AT heqingyao referencegenomesofthetwocultivatedjutespecies AT linlihui referencegenomesofthetwocultivatedjutespecies AT fangpingping referencegenomesofthetwocultivatedjutespecies AT zhangliemei referencegenomesofthetwocultivatedjutespecies AT mingray referencegenomesofthetwocultivatedjutespecies AT qijianmin referencegenomesofthetwocultivatedjutespecies AT zhangliwu referencegenomesofthetwocultivatedjutespecies |