An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
An improved assembly and annotation of the allohexaploid wheat genome identifies complete families of agronomic genes and provides genomic evidence for chromosomal translocations
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DOI：
10.1101/080796
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发表时间：
2016-10
期刊：
影响因子：
7
通讯作者：
Bernardo J. Clavijo;Luca Venturini;Christian Schudoma;G. G. Accinelli-G.;G. Kaithakottil;Jonathan Wright;P. Borrill;George Kettleborough;D. Heavens;Helen Chapman;J. Lipscombe;Tom Barker;Fu-Hao Lu;N. McKenzie;Dina Raats;R. Ramirez-Gonzalez;Aurore Coince;Ned Peel;Lawrence Percival-Alwyn;Owen Duncan;Josua Trösch;Guotai Yu;D. Bolser;Guy Namaati;A. Kerhornou;M. Spannagl;H. Gundlach;G. Haberer;Robert P. Davey;Christine Fosker;F. Palma;A. Phillips;A. Millar;P. Kersey;C. Uauy;K. Krasileva;D. Swarbreck;M. Bevan;M. Clark
中科院分区：
文献类型：
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作者：
Bernardo J. Clavijo;Luca Venturini;Christian Schudoma;G. G. Accinelli-G.;G. Kaithakottil;Jonathan Wright;P. Borrill;George Kettleborough;D. Heavens;Helen Chapman;J. Lipscombe;Tom Barker;Fu-Hao Lu;N. McKenzie;Dina Raats;R. Ramirez-Gonzalez;Aurore Coince;Ned Peel;Lawrence Percival-Alwyn;Owen Duncan;Josua Trösch;Guotai Yu;D. Bolser;Guy Namaati;A. Kerhornou;M. Spannagl;H. Gundlach;G. Haberer;Robert P. Davey;Christine Fosker;F. Palma;A. Phillips;A. Millar;P. Kersey;C. Uauy;K. Krasileva;D. Swarbreck;M. Bevan;M. Clark
基因组测序和组装技术的进步正在产生许多高质量的基因组序列，但大型、重复丰富的多倍体基因组（例如面包小麦的基因组）的组装仍然支离破碎且不完整。我们结合优化的数据类型和旨在处理大型复杂基因组的组装算法，生成了一种新的小麦全基因组鸟枪序列组装。新的组装代表了超过 78% 的基因组，支架 N50 为 88.8kbp，对输入数据具有高保真度。我们的新注释结合了链特异性 Illumina RNAseq 和 PacBio 全长 cDNA，可识别 104,091 个高置信度蛋白质编码基因和 10,156 个非编码 RNA 基因。我们确认了三种已知的基因组重排，并鉴定了一种新的基因组重排。我们的方法能够快速、可扩展地组装小麦基因组、识别结构变异以及定义完整的基因模型，这些都是用于这一全球关键作物的性状分析和育种的强大资源。 [本文提供了补充材料。]
Advances in genome sequencing and assembly technologies are generating many high quality genome sequences, but assemblies of large, repeat-rich polyploid genomes, such as that of bread wheat, remain fragmented and incomplete. We have generated a new wheat whole-genome shotgun sequence assembly using a combination of optimised data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents more than 78% of the genome with a scaffold N50 of 88.8kbp that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNAseq and PacBio full-length cDNAs to identify 104,091 high confidence protein-coding genes and 10,156 non-coding RNA genes. We confirmed three known and identified one novel genome rearrangements. Our approach enables the rapid and scalable assembly of wheat genomes, the identification of structural variants, and the definition of complete gene models, all powerful resources for trait analysis and breeding of this key global crop. [Supplemental material is available for this article.]