Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae)
Characterization and high cross-species transferability of microsatellite markers from the floral transcriptome of Aspidistra saxicola (Asparagaceae)
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Aspidistra saxicola（天冬酰胺科）花转录组微卫星标记的表征和高跨物种可转移性
DOI：
10.1111/1755-0998.12197
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发表时间：
2014-05-01
影响因子：
7.7
通讯作者：
Chen, Jiakuan
中科院分区：
文献类型：
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作者：
Huang, Danni;Zhang, Yiqing;Chen, Jiakuan
利用下一代测序（NGS）技术生成的转录组序列的最新研究已经证明了快速检测和表征来自不同植物的数千个基于基因的微卫星的能力。然而，这些简单重复序列（SSR）很少被直接用于测试种间转移密切相关的物种的群体。蜘蛛抱蛋是一个物种丰富、花结构多样的单子叶植物属，但其鲜花材料不易获得。到目前为止，人们对蜘蛛抱蛋属物种的遗传背景知之甚少，除了它们自然栖息地的可怕减少。本研究利用NGS技术获得了寒地蜘蛛抱蛋花的转录组。根据这些数据，在单基因中共鉴定出5527个SSR。在这些SSR标记中，二核苷酸重复和三核苷酸重复所占的比例相当接近（49.6%对46.8%），其中三核苷酸重复以AGG/CCT最多，其次是AAG/CTT和AGC/GCT，与其他被子植物有明显的差异。为了评估蜘蛛抱蛋属物种的遗传多样性，48个SSR位点进行了测试，在4个可用的人群A. elatior。结果表明，超过三分之一的位点是多态的。这些引物中的大多数在蜘蛛抱蛋属24个种中均能扩增出特异性条带。转录组数据的引物子集被证明是非常有用的检测多态性的相关物种，支持NGS是一种有效的方法，分子标记的发展，在物种内和物种间的水平，特别是在濒危的非模式物种的发现。
Recent studies utilizing transcriptome sequences generated by next-generation sequencing (NGS) technologies have demonstrated the ability to rapidly detect and characterize thousands of gene-based microsatellites from different plants. However, these simple sequence repeats (SSRs) were seldom used directly to test interspecific transferability in the populations of closely related species. Aspidistra Ker-Gawl. is a monocot genus with high species richness and diversity in flower structure, but its fresh floral materials are not easy to obtain. Until now, little is known about genetic background in the species of Aspidistra, quite apart from the fearful reduction of their natural habitats. In this study, the floral transcriptome of Aspidistrasaxicola was obtained using NGS. Based on these data, a total of 5527 SSRs were identified in the unigenes. Among these SSRs, the proportions of di- and tri-nucleotide repeats were quite close (49.6% verse 46.8%), and the most tri-nucleotide repeats were AGG/CCT followed by AAG/CTT and AGC/GCT in A.saxicola, showing distinct differences with other angiosperm species. To assess genetic diversity in the species of Aspidistra, 48 SSR loci were tested in four available populations of A.elatior. The results revealed that more than a third of the loci were polymorphic. The majority of these primers could be amplified in 24 species representing the main clades of Aspidistra. The primer subsets from transcriptome data proved highly useful for detecting polymorphisms in the related species, supporting the finding that NGS is an efficient approach to molecular marker development at both intra- and interspecies levels, especially in endangered nonmodel species.