Separating homeologs by phasing in the tetraploid wheat transcriptome.
Separating homeologs by phasing in the tetraploid wheat transcriptome.
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DOI：
10.1186/gb-2013-14-6-r66
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发表时间：
2013-06-25
期刊：
影响因子：
12.3
通讯作者：
Dubcovsky J
中科院分区：
文献类型：
--
作者：
Krasileva KV;Buffalo V;Bailey P;Pearce S;Ayling S;Tabbita F;Soria M;Wang S;IWGS Consortium;Akhunov E;Uauy C;Dubcovsky J
四倍体面食小麦中重复同源基因组的高度同一性对从头转录组组装提出了重大挑战。为了解决这个问题，我们开发了一个专门的生物信息学工作流程，优化转录组组装和合并同源物的分离。为了评估我们的策略，我们对意大利小麦的一个二倍体祖先的转录组进行了测序和组装，并将这两个组装与13472个全长非冗余面包小麦cdna的基准集进行了比较。来自四倍体小麦的4.89亿个100 bp的成对末端reads聚集在140118个contigs中，包括96%的基准cdna。我们使用比较基因组学方法对66,633个开放阅读框进行了注释。相对于最佳的单个k-mer大小，多重k-mer组装策略使cdna在单个序列中全长组装的比例增加了22%。同源物的分离使用装配后管道，包括多态性鉴定、snp的分阶段、读取排序和分阶段读取的重新组装。使用一组参考基因，我们确定98.7%的SNPs分析是正确的分相。本研究表明，与二倍体小麦相比，四倍体小麦的从头转录组组装更受益于多种k-mer组装策略。我们的研究结果还表明，最初为杂合二倍体生物设计的分相方法可以用于分离四倍体小麦的近同源基因组。预测的四倍体小麦蛋白质组和基因模型为小麦研究界和对比较基因组研究感兴趣的人提供了一个有价值的工具。
The high level of identity among duplicated homoeologous genomes in tetraploid pasta wheat presents substantial challenges for de novo transcriptome assembly. To solve this problem, we develop a specialized bioinformatics workflow that optimizes transcriptome assembly and separation of merged homoeologs. To evaluate our strategy, we sequence and assemble the transcriptome of one of the diploid ancestors of pasta wheat, and compare both assemblies with a benchmark set of 13,472 full-length, non-redundant bread wheat cDNAs. A total of 489 million 100 bp paired-end reads from tetraploid wheat assemble in 140,118 contigs, including 96% of the benchmark cDNAs. We used a comparative genomics approach to annotate 66,633 open reading frames. The multiple k-mer assembly strategy increases the proportion of cDNAs assembled full-length in a single contig by 22% relative to the best single k-mer size. Homoeologs are separated using a post-assembly pipeline that includes polymorphism identification, phasing of SNPs, read sorting, and re-assembly of phased reads. Using a reference set of genes, we determine that 98.7% of SNPs analyzed are correctly separated by phasing. Our study shows that de novo transcriptome assembly of tetraploid wheat benefit from multiple k-mer assembly strategies more than diploid wheat. Our results also demonstrate that phasing approaches originally designed for heterozygous diploid organisms can be used to separate the close homoeologous genomes of tetraploid wheat. The predicted tetraploid wheat proteome and gene models provide a valuable tool for the wheat research community and for those interested in comparative genomic studies.
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影响因子：
56.9
作者：
Carninci, P;Kasukawa, T;Hayashizaki, Y
通讯作者：
Hayashizaki, Y
影响因子：
3.3
作者：
Dvorak, J;Yang, ZL;Luo, MC
通讯作者：
Luo, MC
影响因子：
4.4
作者：
Cantu D;Vanzetti LS;Sumner A;Dubcovsky M;Matvienko M;Distelfeld A;Michelmore RW;Dubcovsky J
通讯作者：
Dubcovsky J
影响因子：
4.4
作者：
Cantu D;Pearce SP;Distelfeld A;Christiansen MW;Uauy C;Akhunov E;Fahima T;Dubcovsky J
通讯作者：
Dubcovsky J
影响因子：
7.4
作者：
Akhunov, Eduard D.;Sehgal, Sunish;Gill, Bikram S.
通讯作者：
Gill, Bikram S.