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A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near‐complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nan...

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Detalles Bibliográficos
Autores principales: Zhang, Lei, Liang, Jianli, Chen, Haixu, Zhang, Zhicheng, Wu, Jian, Wang, Xiaowu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10106856/
https://www.ncbi.nlm.nih.gov/pubmed/36688739
http://dx.doi.org/10.1111/pbi.14015
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author Zhang, Lei
Liang, Jianli
Chen, Haixu
Zhang, Zhicheng
Wu, Jian
Wang, Xiaowu
author_facet Zhang, Lei
Liang, Jianli
Chen, Haixu
Zhang, Zhicheng
Wu, Jian
Wang, Xiaowu
author_sort Zhang, Lei
collection PubMed
description Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near‐complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong‐read sequencing and Hi‐C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near‐complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.
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spelling pubmed-101068562023-04-18 A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres Zhang, Lei Liang, Jianli Chen, Haixu Zhang, Zhicheng Wu, Jian Wang, Xiaowu Plant Biotechnol J Research Articles Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near‐complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong‐read sequencing and Hi‐C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near‐complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres. John Wiley and Sons Inc. 2023-02-02 2023-05 /pmc/articles/PMC10106856/ /pubmed/36688739 http://dx.doi.org/10.1111/pbi.14015 Text en © 2023 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, Lei
Liang, Jianli
Chen, Haixu
Zhang, Zhicheng
Wu, Jian
Wang, Xiaowu
A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title_full A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title_fullStr A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title_full_unstemmed A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title_short A near‐complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres
title_sort near‐complete genome assembly of brassica rapa provides new insights into the evolution of centromeres
topic Research Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10106856/
https://www.ncbi.nlm.nih.gov/pubmed/36688739
http://dx.doi.org/10.1111/pbi.14015
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