Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping
Characterization of duplicate gene evolution in the recent natural allopolyploid Tragopogon miscellus by next-generation sequencing and Sequenom iPLEX MassARRAY genotyping
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DOI：
10.1111/j.1365-294x.2009.04469.x
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发表时间：
2010-03-01
影响因子：
4.9
通讯作者：
Barbazuk, W. Brad
中科院分区：
文献类型：
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作者：
Buggs, Richard J. A.;Chamala, Srikar;Barbazuk, W. Brad
芒叶婆罗门参（菊科）是研究自然异源多倍性的进化模式，但迄今为止作为遗传模式的资源不足。利用454和Illumina表达序列标签对二倍体T.通过比较，我们鉴定了7782个单核苷酸多态性，这些多态性在这个异源四倍体中存在的两个祖先基因组之间存在差异。使用Sequenom MassARRAY iPlex基因分型对基因组DNA中98个SNP的样品进行验证，在基因组水平上确认了92个SNP标记，这些标记可诊断两个亲本基因组。在单个T. miscellus叶中，使用Illumina测序，69%的SNP显示两种同源物（来自不同亲本的重复同源基因）的大致相等表达，22%显示明显差异表达，8.5%显示一种同源物在T.混合物。大多数同源基因沉默的病例涉及T。Alcohus SNP同源物（1.64/254; 65%）而不是T. pratensis homeolog（90/254）。基因组DNA的序列组分析显示，在27个显示明显沉默的同源物的样品中，23（85（V（，））是由于基因组同源物丢失。这些方法可以应用于任何生物体，允许高效且具有成本效益的遗传标记生成。
Tragopogon miscellus (Asteraceae) is an evolutionary model for the study of natural allopolyploidy, but until now has been under-resourced as a genetic model. Using 454 and Illumina expressed sequence tag sequencing of the parental diploid species of T. miscellus, we identified 7782 single nucleotide polymorphisms that differ between the two progenitor genomes present in this allotetraploid. Validation of a sample of 98 of these SNPs in genomic DNA using Sequenom MassARRAY iPlex genotyping confirmed 92 SNP markers at the genomic level that were diagnostic for the two parental genomes. In a transcriptome profile of 2989 SNPs in a single T. miscellus leaf, using Illumina sequencing, 69% of SNPs showed approximately equal expression of both homeologs (duplicate homologous genes derived from different parents), 22% showed apparent differential expression and 8.5% showed apparent silencing of one homeolog in T. miscellus. The majority of cases of homeolog silencing involved the T. dubius SNP homeolog (1.64/254; 65%) rather than the T. pratensis homeolog (90/254). Sequenom analysis of genomic DNA showed that in a sample of 27 of the homeologs showing apparent silencing, 23 (85(V(,) were because of genomic homeolog loss. These methods could be applied to any organism, allowing efficient and cost-effective generation of genetic markers.