Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.
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DOI：
10.1093/bioinformatics/btt178
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发表时间：
2013-06-15
期刊：
影响因子：
--
通讯作者：
Jones SJ
中科院分区：
文献类型：
--
作者：
Birol I;Raymond A;Jackman SD;Pleasance S;Coope R;Taylor GA;Yuen MM;Keeling CI;Brand D;Vandervalk BP;Kirk H;Pandoh P;Moore RA;Zhao Y;Mungall AJ;Jaquish B;Yanchuk A;Ritland C;Boyle B;Bousquet J;Ritland K;Mackay J;Bohlmann J;Jones SJ
白云杉（Picea glauca）是北美北方森林的主要针叶树，为这种具有商业价值的树木提供基因组学资源将有助于改善森林管理和保护工作。测序和组装大型和高度重复的云杉基因组推动了当前技术的边界。在这里，我们描述了使用两个Illumina测序平台的全基因组霰弹枪测序策略和使用ABySS软件的组装方法。我们在490万个支架中报告了20.8千兆碱基对的基因组草图，支架N50为20356bp。我们展示了最近测序技术的改进，特别是增加的读取长度和来自较长片段的成对末端读取对组装的连续性有重大影响。我们还注意到，可扩展的生物信息学工具有助于提供快速草案组件。可获得性：云杉基因组测序和组装数据可通过NCBI获得（登录号：ALWZ0100000000 PID: PRJNA83435）。http://www.ncbi.nlm.nih.gov/bioproject/83435。补充信息：补充数据可在Bioinformatics在线获取。
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20 356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies. Availability: The Picea glauca genome sequencing and assembly data are available through NCBI (Accession#: ALWZ0100000000 PID: PRJNA83435). http://www.ncbi.nlm.nih.gov/bioproject/83435. Contact: ibirol@bcgsc.ca Supplementary information: Supplementary data are available at Bioinformatics online.
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影响因子：
4.4
作者：
Ralph SG;Chun HJ;Kolosova N;Cooper D;Oddy C;Ritland CE;Kirkpatrick R;Moore R;Barber S;Holt RA;Jones SJ;Marra MA;Douglas CJ;Ritland K;Bohlmann J
通讯作者：
Bohlmann J
影响因子：
7
作者：
Ribeiro FJ;Przybylski D;Yin S;Sharpe T;Gnerre S;Abouelleil A;Berlin AM;Montmayeur A;Shea TP;Walker BJ;Young SK;Russ C;Nusbaum C;MacCallum I;Jaffe DB
通讯作者：
Jaffe DB
影响因子：
12.3
作者：
Keeling CI;Yuen MM;Liao NY;Docking TR;Chan SK;Taylor GA;Palmquist DL;Jackman SD;Nguyen A;Li M;Henderson H;Janes JK;Zhao Y;Pandoh P;Moore R;Sperling FA;Huber DP;Birol I;Jones SJ;Bohlmann J
通讯作者：
Bohlmann J
影响因子：
1.1
作者：
Ferragina, Paolo;Gagie, Travis;Manzini, Giovanni
通讯作者：
Manzini, Giovanni
影响因子：
7.4
作者：
Keeling, Christopher I.;Dullat, Harpreet K.;Bohlmann, Joerg
通讯作者：
Bohlmann, Joerg