HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.
HANDS2: accurate assignment of homoeallelic base-identity in allopolyploids despite missing data.
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DOI：
10.1038/srep29234
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发表时间：
2016-07-05
影响因子：
4.6
通讯作者：
Mithani A
中科院分区：
文献类型：
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作者：
Khan A;Belfield EJ;Harberd NP;Mithani A
异源多倍体的同源等位基因碱基同一性的表征是困难的，因为同源亚基因组是密切相关的，如果二倍体-祖先数据丢失，则会变得更加具有挑战性。我们提出了HANDS2，这是一种基于下一代测序的工具，即使在没有二倍体祖先的情况下，它也能够在全基因组范围内高度准确(90%)地发现异源多倍体中同源基因特有的碱基同一性。我们将HANDS2应用于十字花科油菜属植物的转录本研究。我们的结果表明，甘蓝型油菜的三个C基因组比三个A基因组更相似，并在单碱基分辨率下对不同的甘蓝型四倍体及其二倍体祖先之间的关系提供了重要的见解。
Characterization of homoeallelic base-identity in allopolyploids is difficult since homeologous subgenomes are closely related and becomes further challenging if diploid-progenitor data is missing. We present HANDS2, a next-generation sequencing-based tool that enables highly accurate (>90%) genome-wide discovery of homeolog-specific base-identity in allopolyploids even in the absence of a diploid-progenitor. We applied HANDS2 to the transcriptomes of various cruciferous plants belonging to genus Brassica. Our results suggest that the three C genomes in Brassica are more similar to each other than the three A genomes, and provide important insights into the relationships between various Brassica tetraploids and their diploid-progenitors at a single-base resolution.