A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis

The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were d...

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Autores principales: Yang, Xuchen, Kang, Minghui, Yang, Yanting, Xiong, Haifeng, Wang, Mingcheng, Zhang, Zhiyang, Wang, Zefu, Wu, Haolin, Ma, Tao, Liu, Jianquan, Xi, Zhenxiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2019
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Data Descriptor
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6877568/
https://www.ncbi.nlm.nih.gov/pubmed/31767848
http://dx.doi.org/10.1038/s41597-019-0296-y
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author Yang, Xuchen
Kang, Minghui
Yang, Yanting
Xiong, Haifeng
Wang, Mingcheng
Zhang, Zhiyang
Wang, Zefu
Wu, Haolin
Ma, Tao
Liu, Jianquan
Xi, Zhenxiang
author_facet Yang, Xuchen
Kang, Minghui
Yang, Yanting
Xiong, Haifeng
Wang, Mingcheng
Zhang, Zhiyang
Wang, Zefu
Wu, Haolin
Ma, Tao
Liu, Jianquan
Xi, Zhenxiang
author_sort Yang, Xuchen
collection PubMed
description The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were de novo assembled into 647 polished contigs with a total length of 1,001.42 megabases (Mb) and an N50 size of 3.62 Mb, which is in line with genome sizes estimated using flow cytometry and the k-mer analysis. These contigs were further clustered and ordered into 22 pseudo-chromosomes based on Hi-C data, matching the chromosome counts in Nyssa obtained from previous cytological studies. In addition, a total of 664.91 Mb of repetitive elements were identified and a total of 37,884 protein-coding genes were predicted in the genome of N. sinensis. All data were deposited in publicly available repositories, and should be a valuable resource for genomics, evolution, and conservation biology.
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spelling pubmed-68775682019-12-03 A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis Yang, Xuchen Kang, Minghui Yang, Yanting Xiong, Haifeng Wang, Mingcheng Zhang, Zhiyang Wang, Zefu Wu, Haolin Ma, Tao Liu, Jianquan Xi, Zhenxiang Sci Data Data Descriptor The deciduous Chinese tupelo (Nyssa sinensis Oliv.) is a popular ornamental tree for the spectacular autumn leaf color. Here, using single-molecule sequencing and chromosome conformation capture data, we report a high-quality, chromosome-level genome assembly of N. sinensis. PacBio long reads were de novo assembled into 647 polished contigs with a total length of 1,001.42 megabases (Mb) and an N50 size of 3.62 Mb, which is in line with genome sizes estimated using flow cytometry and the k-mer analysis. These contigs were further clustered and ordered into 22 pseudo-chromosomes based on Hi-C data, matching the chromosome counts in Nyssa obtained from previous cytological studies. In addition, a total of 664.91 Mb of repetitive elements were identified and a total of 37,884 protein-coding genes were predicted in the genome of N. sinensis. All data were deposited in publicly available repositories, and should be a valuable resource for genomics, evolution, and conservation biology. Nature Publishing Group UK 2019-11-25 /pmc/articles/PMC6877568/ /pubmed/31767848 http://dx.doi.org/10.1038/s41597-019-0296-y Text en © The Author(s) 2019 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the metadata files associated with this article.
spellingShingle Data Descriptor
Yang, Xuchen
Kang, Minghui
Yang, Yanting
Xiong, Haifeng
Wang, Mingcheng
Zhang, Zhiyang
Wang, Zefu
Wu, Haolin
Ma, Tao
Liu, Jianquan
Xi, Zhenxiang
A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title_full A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title_fullStr A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title_full_unstemmed A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title_short A chromosome-level genome assembly of the Chinese tupelo Nyssa sinensis
title_sort chromosome-level genome assembly of the chinese tupelo nyssa sinensis
topic Data Descriptor
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6877568/
https://www.ncbi.nlm.nih.gov/pubmed/31767848
http://dx.doi.org/10.1038/s41597-019-0296-y
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