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利用纳米孔测序技术构建无间隙端粒到端粒的香蕉染色体。

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing.

机构信息

Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ Evry, Université Paris-Saclay, Evry, France.

CIRAD, UMR AGAP Institut, Montpellier, France.

出版信息

Commun Biol. 2021 Sep 7;4(1):1047. doi: 10.1038/s42003-021-02559-3.

DOI:10.1038/s42003-021-02559-3
PMID:34493830
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8423783/
Abstract

Long-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

摘要

长读技术有望获得更完整的基因组组装，并使组装变得更加容易。与长程技术相结合，它们可以揭示复杂区域的结构，如着丝粒或 rDNA 簇。这些技术还可以了解染色体的完整结构，即使使用遗传图谱，这在以前也是非常复杂的。然而，生成无间隙且端粒到端粒的组装仍然不容易，需要结合多种技术并选择合适的软件。在这里，我们报告了使用牛津纳米孔长读序列生成的香蕉基因组（Musa acuminata）的染色体水平组装。我们从单个 PromethION 流动池生成了 177X 的基因组覆盖度，其中近 17X 的读长大于 75 kbp。在 11 条染色体中，有 5 条从端粒到端粒完全重建在单个连续体中，首次揭示了着丝粒或同源基因簇等复杂区域的内容。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/418dcd364836/42003_2021_2559_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/3b69b8ff05bc/42003_2021_2559_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/fd23afa599fb/42003_2021_2559_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/269cd2bb89ad/42003_2021_2559_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/418dcd364836/42003_2021_2559_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/3b69b8ff05bc/42003_2021_2559_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/fd23afa599fb/42003_2021_2559_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/269cd2bb89ad/42003_2021_2559_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f3c5/8423783/418dcd364836/42003_2021_2559_Fig4_HTML.jpg

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