State Key Laboratory of Bio-control and Guangdong Provincial Key Laboratory of Plant Resources, Sun Yat-sen University, Guangzhou, 510275, China.
Department of Biology, Vietnam National Museum of Nature, Vietnam Academy of Science and Technology, 18 Hoang Quo Viet, Cau Giay, Ha Noi, Vietnam.
Mol Biol Rep. 2019 Dec;46(6):6547-6556. doi: 10.1007/s11033-019-05106-w. Epub 2019 Oct 3.
Rhodoleia Champion 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 for R. championii to 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 of R. 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 three Rhodoleia species showed that 32 and 40 SSR markers can be amplified in Vietnam and Jinping populations of R. parvipetala, 41, 33, and 41 SSR markers in Boluo, Hongkong and Xinyi populations of R. championii, 25 SSR markers in Fugong population of R. 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 (H) ranged from 0.000 to 1.000, and expected heterozygosity (H) ranged from 0.091 to 0.851. In the present study, we provided the first whole-genome sequencing database for the species R. championii, identified ample SSR loci with designed primers, and revealed that 20 of the 110 selected SSRs were polymorphic across three Rhodoleia species. These provide valuable resources for future studies on genetic study, species delimitation, phylogeography, and conservation of this genus.
金缕梅科是理解开花植物起源和早期进化的关键科之一，其中的伯乐树属是最原始的孑遗属之一。本研究为伯乐树属（Rhodoleia Champion ex Hooker）开发了基因组简单重复序列（SSR），以进行该属的遗传多样性、系统发生结构或系统进化研究。在对伯乐树属进行的低覆盖度全基因组测序的从头组装的 278743 条序列（105758242 bp）中，共检测到 8370 条序列中存在 9106 个 SSR，成功设计了 6677 对 SSR 引物。在 110 对引物中，41 对在 SSR 筛选的初步测试中成功扩增。进一步对来自伯乐树属三个种的六个种群的 122 个个体进行这 41 对引物的扩增，结果表明，在越南和金平种群的 R. parvipetala 中可扩增出 32 对和 40 对 SSR 标记，在博罗、香港和新沂种群的 R. championii 中可扩增出 41 对、33 对和 41 对 SSR 标记，在佛冈种群的 R. forrestii 中可扩增出 25 对 SSR 标记，在三个种中都能扩增出 20 对具有多态性的 SSR 标记。对这 20 对多态性 SSR 的遗传分析表明，等位基因数（A）在四个到 13 之间，多态性信息含量（PIC）在三个种之间的范围为 0.479 到 0.876。在种群水平上，观测杂合度（H）在 0.000 到 1.000 之间，期望杂合度（H）在 0.091 到 0.851 之间。本研究首次为伯乐树属提供了全基因组测序数据库，鉴定出大量具有设计引物的 SSR 位点，并发现 110 对 SSR 中 20 对在三个伯乐树属种之间具有多态性。这些为该属的遗传研究、物种划分、系统发生地理和保护提供了有价值的资源。
