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/gr.217117.116
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发表时间：
2017-05
期刊：
影响因子：
7
通讯作者：
Clark MD
中科院分区：
文献类型：
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作者：
Clavijo BJ;Venturini L;Schudoma C;Accinelli GG;Kaithakottil G;Wright J;Borrill P;Kettleborough G;Heavens D;Chapman H;Lipscombe J;Barker T;Lu FH;McKenzie N;Raats D;Ramirez-Gonzalez RH;Coince A;Peel N;Percival-Alwyn L;Duncan O;Trösch J;Yu G;Bolser DM;Namaati G;Kerhornou A;Spannagl M;Gundlach H;Haberer G;Davey RP;Fosker C;Palma FD;Phillips AL;Millar AH;Kersey PJ;Uauy C;Krasileva KV;Swarbreck D;Bevan MW;Clark MD
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的组装，如面包小麦的组装，仍然是碎片化和不完整的。我们已经产生了一个新的小麦全基因组鸟枪序列组装使用优化的数据类型和组装算法的组合，旨在处理大型和复杂的基因组。新组装体代表>78%的基因组，具有88.8kb的支架N50，其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 RNA-seq和Pacific Biosciences（PacBio）全长cDNA，以识别104，091个高置信度的蛋白质编码基因和10，156个非编码RNA基因。我们证实了三个已知的，并确定了一个新的基因组重排。我们的方法能够快速和可扩展地组装小麦基因组，识别结构变体，并定义完整的基因模型，所有这些都是这一关键全球作物的性状分析和育种的强大资源。
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 optimized data types and an assembly algorithm designed to deal with large and complex genomes. The new assembly represents >78% of the genome with a scaffold N50 of 88.8 kb that has a high fidelity to the input data. Our new annotation combines strand-specific Illumina RNA-seq and Pacific Biosciences (PacBio) full-length cDNAs to identify 104,091 high-confidence protein-coding genes and 10,156 noncoding 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.