Development and characterization of genomic microsatellite markers in the tree species, Rhodoleia championii, R. parvipetala, and R. forrestii (Hamamelidaceae)
Development and characterization of genomic microsatellite markers in the tree species, Rhodoleia championii, R. parvipetala, and R. forrestii (Hamamelidaceae)
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树种红杜鹃、R. parvipetala 和 R. forrestii（金缕梅科）基因组微卫星标记的开发和表征
DOI：
10.1007/s11033-019-05106-w
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发表时间：
2019
影响因子：
2.8
通讯作者：
Fan Qiang
中科院分区：
文献类型：
--
作者：
Huang Yanshuang;Yin Qianyi;Van Truong Do;Meng Kaikai;Chen Sufang;Liao Boyong;Fan Qiang
RhodoleiaChampion ex Hooker 是金缕梅科最原始的孑遗属之一，金缕梅科是了解开花植物起源和早期进化的关键科。基因组简单序列重复 (SSR) 是为 R 开发的。 Championiito 对该属进行遗传多样性、系统发育地理结构甚至系统进化研究。在R的低覆盖率全基因组测序中从头组装的278,743个重叠群（105,758,242 bps）中。在championii中，在8370个重叠群中总共检测到9106个SSR，并成功设计了6677个SSR的SSR引物对。筛选的110对引物中，有41对在SSR筛选初试中扩增成功。对从三个红杜鹃属物种的 6 个种群收集的 122 个个体中进一步扩增这 41 个引物对表明，可以在越南和锦屏红杜鹃种群中扩增 32 和 40 个 SSR 标记。博罗、香港和信宜种群的 parvipetala、41、33 和 41 SSR 标记。 Championii，R.福贡群体中的25个SSR标记。 forrestii 和 20 个 SSR 标记被证明在这三个物种中具有多态性。对这 20 个多态性 SSR 的遗传分析表明，这三个物种的等位基因数 (A) 范围为 4 至 13，多态信息含量 (PIC) 范围为 0.479 至 0.876。在群体水平上，观察到的杂合度（HO）范围为0.000至1.000，预期杂合度（HE）范围为0.091至0.851。在本研究中，我们提供了第一个物种R的全基因组测序数据库。 Championii 用设计的引物鉴定了充足的 SSR 位点，并揭示了 110 个选定的 SSR 中的 20 个在三个红豆属物种中具有多态性。这些为未来该属的遗传研究、物种界定、系统发育地理学和保护等研究提供了宝贵的资源。
RhodoleiaChampion ex Hooker is one of the most primitive relict genera of Hamamelidaceae, a key family exploited to understand the origin and early evolution of flowering plants. Genomic simple sequence repeats (SSRs) were developed forR. championiito perform genetic diversity, phylogeographical structure or even systematic evolution studies of the genus. Among the 278,743 contigs (105,758,242 bps) de novo assembled from the low-coverage whole genome sequencing ofR. championii, a total of 9106 SSRs were detected in 8370 contigs, and SSR primer pairs were successfully designed for 6677 SSRs. Among the 110 selected primer pairs, 41 were amplified successfully in the preliminary test of SSR screening. Further amplification of these 41 primer pairs across the 122 individuals collected from six populations of the threeRhodoleiaspecies showed that 32 and 40 SSR markers can be amplified in Vietnam and Jinping populations ofR. parvipetala, 41, 33, and 41 SSR markers in Boluo, Hongkong and Xinyi populations ofR. championii, 25 SSR markers in Fugong population ofR. forrestii, and 20 SSR markers demonstrated to be polymorphic across the three species. Genetic analysis for these 20 polymorphic SSRs showed that Allele number (A) ranged from four to 13 and polymorphic information content (PIC) ranged from 0.479 to 0.876 across the three species. At the population level, observed heterozygosity (HO) ranged from 0.000 to 1.000, and expected heterozygosity (HE) ranged from 0.091 to 0.851. In the present study, we provided the first whole-genome sequencing database for the speciesR. championii, identified ample SSR loci with designed primers, and revealed that 20 of the 110 selected SSRs were polymorphic across threeRhodoleiaspecies. These provide valuable resources for future studies on genetic study, species delimitation, phylogeography, and conservation of this genus.