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首页> 外文期刊>Proceedings of the National Academy of Sciences of the United States of America >Reference-assisted chromosome assembly
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Reference-assisted chromosome assembly

机译：参考辅助染色体组装

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摘要

One of the most difficult problems in modern genomics is the assembly of full-length chromosomes using next generation sequencing (NGS) data. To address this problem, we developed "reference-assisted chromosome assembly" (RACA), an algorithm to reliably order and orient sequence scaffolds generated by NGS and assemblers into longer chromosomal fragments using comparative genome information and paired-end reads. Evaluation of results using simulated and real genome assemblies indicates that our approach can substantially improve genomes generated by a wide variety of de novo assemblers if a good reference assembly of a closely related species and outgroup genomes are available. We used RACA to reconstruct 60 Tibetan antelope (Pantholops hodgso-nii) chromosome fragments from 1,434 SOAPdenovo sequence scaffolds, of which 16 chromosome fragments were homologous to complete cattle chromosomes. Experimental validation by PCR showed that predictions made by RACA are highly accurate. Our results indicate that RACA will significantly facilitate the study of chromosome evolution and genome rearrangements for the large number of genomes being sequenced by NGS that do not have a genetic or physical map.
机译：现代基因组学中最困难的问题之一是使用下一代测序（NGS）数据组装全长染色体。为了解决此问题，我们开发了“参考辅助染色体组装”（RACA），该算法可使用比较基因组信息和配对末端读数，将由NGS和组装者生成的序列支架可靠地排序和定向为更长的染色体片段。使用模拟和真实基因组装配对结果进行的评估表明，如果可以使用密切相关的物种和外基因组的良好参考装配，我们的方法可以大大改善由各种各样的从头装配商产生的基因组。我们使用RACA从1,434个SOAPdenovo序列支架中重建了60个藏羚羊（Pantholops hodgso-nii）染色体片段，其中16个染色体片段与完整的牛染色体同源。通过PCR进行的实验验证表明，RACA所做的预测非常准确。我们的结果表明，RACA将极大地促进研究NGS测序的大量基因组的染色体进化和基因组重排，而这些基因组没有遗传或物理图谱。

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  • 作者

    Jaebum Kim; Denis M. Larkin; Qingle Cai; Asan; Yongfen Zhang; Ri-Li Ge; Loretta Auvil; Boris Capitanu; Guojie Zhang; Harris A. Lewin; Jian Ma;

  • 作者单位

    Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,Department of Animal Biotechnology, Konkuk University, Seoul 143-701, Korea;

    Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Aberystwyth, Ceredigion SY23 3DA, United Kingdom;

    Beijing Genomics Institute, Shenzhen 518083, China;

    Beijing Genomics Institute, Shenzhen 518083, China;

    Beijing Genomics Institute, Shenzhen 518083, China;

    Key Laboratory for High Altitude Medicine, Ministry of Chinese Education and Research Center for High Altitude Medicine, Qinghai University, Xining, Qinghai 810001, China;

    National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61802;

    National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Urbana, IL 61801,Illinois Informatics Institute, University of Illinois at Urbana-Champaign, Urbana, IL 61802;

    Beijing Genomics Institute, Shenzhen 518083, China;

    Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,Department of Evolution and Ecology, University of California, Davis, CA 95616;

    Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801,Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL 61801;

  • 收录信息 美国《科学引文索引》(SCI);美国《生物学医学文摘》(MEDLINE);美国《化学文摘》(CA);
  • 原文格式 PDF
  • 正文语种 eng
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  • 关键词

    computational genomics; comparative genomics; bioinformatics; chromosome breakpoints; mammals;

    机译：计算基因组学;比较基因组学;生物信息学染色体断点;哺乳动物;

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