Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley

Xingquan Zeng, View ORCID ProfileXiangfeng Li, Lijun Bai, Yulin Wang, Tong Xu, Hongjun Yuan, Qijun Xu, Sang Zha, Zexiu Wei, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzai Yu, Tashi Nyima
doi: https://doi.org/10.1101/409136
Xingquan Zeng
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Xiangfeng Li
5Chengdu Life Baseline Technology Co., LTD, Chengdu 610041, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • ORCID record for Xiangfeng Li
Lijun Bai
5Chengdu Life Baseline Technology Co., LTD, Chengdu 610041, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yulin Wang
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tong Xu
5Chengdu Life Baseline Technology Co., LTD, Chengdu 610041, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Hongjun Yuan
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Qijun Xu
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Sang Zha
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Zexiu Wei
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
4Agricultural Resources and Environment Research Institute, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Wangmu Qimei
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Yuzhen Basang
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Jiabu Dunzhu
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Mingzai Yu
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
2Research Institute of Agriculture, Tibet Academy of Agricultural and Animal Husbandry Sciences Lhasa, Tibet 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Tashi Nyima
1State Key Laboratory of Barley and Yak Germplasm Resources and Genetic Improvement, Lhasa 850002, China
3Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: nima_zhaxi@sina.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Supplementary material
  • Preview PDF
Loading

Abstract

Background The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The Qingke in China has about 3500 years of cultivation history, mainly produced in Tibet, Qinghai, Sichuan, Yunnan and other areas. In addition, Qingke has rich nutritional value and outstanding health effects, including the beta glucan, dietary fiber, amylopectin, the contents of trace elements, which are higher than any other cereal crops.

Findings Here, we reported an improved high-quality assembly of Qingke genome with 4.0 Gb in size. We employed the falcon assembly package, scaffolding and error correction tools to finish improvement using PacBio long reads sequencing technology, with contig and scaffold N50 lengths of 1.563Mb and 4.006Mb, respectively, representing more continuous than the original Qingke genome nearly two orders of magnitude. We also reannotated the new assembly, and reported 61,303 stringent confident putative proteincoding genes, of which 40,457 is HC genes. We have developed a new Qingke genome database (QGD) to download and use friendly, as well as to better manage the information of the Qingke genetic resources.

Conclusions The availability of new Qingke genome and annotations will take the genetics of Qingke to a new level and will greatly simplify the breeders effort. It will also enrich the granary of the Tibetan people.

  • Abbreviations

    BLAST
    Basic Local Alignment Search Tool
    BUSCO
    Benchmarking Universal Single-Copy Orthologs
    QV
    quality value
    PacBio
    Pacifc Biosciences
    RNA-seq
    RNA sequencing
    NGS
    Next generation sequencing
    TGS
    Third generation sequencing
    QGD
    Qingke Genome Database
  • Copyright 
    The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. All rights reserved. No reuse allowed without permission.
    Back to top
    PreviousNext
    Posted September 07, 2018.
    Download PDF

    Supplementary Material

    Email

    Thank you for your interest in spreading the word about bioRxiv.

    NOTE: Your email address is requested solely to identify you as the sender of this article.

    Enter multiple addresses on separate lines or separate them with commas.
    An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley
    (Your Name) has forwarded a page to you from bioRxiv
    (Your Name) thought you would like to see this page from the bioRxiv website.
    CAPTCHA
    This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
    Share
    An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley
    Xingquan Zeng, Xiangfeng Li, Lijun Bai, Yulin Wang, Tong Xu, Hongjun Yuan, Qijun Xu, Sang Zha, Zexiu Wei, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzai Yu, Tashi Nyima
    bioRxiv 409136; doi: https://doi.org/10.1101/409136
    Reddit logo Twitter logo Facebook logo LinkedIn logo Mendeley logo
    Citation Tools
    An improved high-quality genome assembly and annotation of Qingke, Tibetan hulless barley
    Xingquan Zeng, Xiangfeng Li, Lijun Bai, Yulin Wang, Tong Xu, Hongjun Yuan, Qijun Xu, Sang Zha, Zexiu Wei, Wangmu Qimei, Yuzhen Basang, Jiabu Dunzhu, Mingzai Yu, Tashi Nyima
    bioRxiv 409136; doi: https://doi.org/10.1101/409136

    Citation Manager Formats

    • BibTeX
    • Bookends
    • EasyBib
    • EndNote (tagged)
    • EndNote 8 (xml)
    • Medlars
    • Mendeley
    • Papers
    • RefWorks Tagged
    • Ref Manager
    • RIS
    • Zotero
    • Tweet Widget
    • Facebook Like
    • Google Plus One

    Subject Area

    • Genomics
    Subject Areas
    All Articles
    • Animal Behavior and Cognition (4685)
    • Biochemistry (10362)
    • Bioengineering (7683)
    • Bioinformatics (26343)
    • Biophysics (13534)
    • Cancer Biology (10694)
    • Cell Biology (15446)
    • Clinical Trials (138)
    • Developmental Biology (8501)
    • Ecology (12824)
    • Epidemiology (2067)
    • Evolutionary Biology (16868)
    • Genetics (11402)
    • Genomics (15484)
    • Immunology (10622)
    • Microbiology (25226)
    • Molecular Biology (10225)
    • Neuroscience (54483)
    • Paleontology (402)
    • Pathology (1669)
    • Pharmacology and Toxicology (2897)
    • Physiology (4345)
    • Plant Biology (9254)
    • Scientific Communication and Education (1587)
    • Synthetic Biology (2558)
    • Systems Biology (6781)
    • Zoology (1466)