Key Laboratory of Plant Resource Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Science, Guangzhou 510650, China.
BMC Genomics. 2013 May 14;14:329. doi: 10.1186/1471-2164-14-329.
Primula species are important early spring garden plants with a centre of diversity and speciation in the East Himalaya-Hengduan Mountains in Western China. Studies on population genetics, speciation and phylogeny of Primula have been impeded by a lack of genomic resources. In the present study, we sequenced the transcriptomes of two closely related primrose species, Primula poissonii and Primula wilsonii, using short reads on the Illumina Genome Analyzer platform.
We obtained 55,284 and 55,011 contigs with N50 values of 938 and 1,085 for P. poissonii and P. wilsonii, respectively, and 6,654 pairs of putative orthologs were identified between the two species. Estimations of non-synonymous/synonymous substitution rate ratios for these orthologs indicated that 877 of the pairs may be under positive selection (Ka/Ks > 0.5), and functional enrichment analysis revealed that significant proportions of the orthologs were in the categories DNA repair, stress resistance, which may provide some hints as to how the two closely related Primula species adapted differentially to extreme environments, such as habitats characterized by aridity, high altitude and high levels of ionizing radiation. It was possible for the first time to estimate the divergence time between the radiated species pair, P. poissonii and P. wilsonii; this was found to be approximately 0.90 ± 0.57 Mya, which falls between the Donau and Gunz glaciation in the Middle Pleistocene. Primers based on 54 pairs of orthologous SSR-containing sequences between the two Primula species were designed and verified. About half of these pairs successfully amplified for both species. Of the 959 single copy nuclear genes shared by four model plants (known as APVO genes), 111 single copy nuclear genes were verified as being present in both Primula species and exon-anchored and intron-spanned primers were designed for use.
We characterized the transcriptomes for the two Primula species, and produced an unprecedented amount of genomic resources for these important garden plants. Evolutionary analysis of these two Primula species not only revealed a more precise divergence time, but also provided some novel insights into how differential adaptations occurred in extreme habitats. Furthermore, we developed two sets of genetic markers, single copy nuclear genes and nuclear microsatellites (EST-SSR). Both these sets of markers will facilitate studies on the genetic improvement, population genetics and phylogenetics of this rapidly adapting taxon.
报春花属植物是重要的早春园林植物，其多样性和物种形成中心位于中国西部的东喜马拉雅-横断山脉。由于缺乏基因组资源，报春花属植物的种群遗传学、物种形成和系统发育研究受到了阻碍。本研究采用 Illumina 基因组分析仪平台对两种亲缘关系密切的报春花（报春花和威尔逊报春花）进行了短读序列转录组测序。
我们分别获得了 55284 个和 55011 个 P. poissonii 和 P. wilsonii 的 contigs，其 N50 值分别为 938 和 1085，并且在这两个物种之间鉴定了 6654 对推定的直系同源基因对。对这些直系同源基因对的非同义/同义取代率比值的估计表明，877 对可能受到正选择（Ka/Ks > 0.5）的影响，功能富集分析表明，相当比例的直系同源基因在 DNA 修复、应激反应等类别中，这可能为这两个亲缘关系密切的报春花属植物如何适应极端环境（如干旱、高海拔和高水平电离辐射的生境）提供了一些线索。首次有可能估计辐射物种对（P. poissonii 和 P. wilsonii）之间的分化时间；研究发现，这大约发生在中更新世的多瑙河和冈兹冰川之间，为 0.90±0.57 Mya。基于这两个报春花物种之间的 54 对含有 SSR 的直系同源序列设计并验证了引物。这些引物中约有一半能成功地同时扩增两个物种。在四个模式植物（称为 APVO 基因）共享的 959 个单拷贝核基因中，有 111 个单拷贝核基因被证实存在于这两个报春花物种中，并设计了外显子锚定和内含子跨越引物。
我们对这两个报春花物种的转录组进行了特征描述，并为这些重要的园林植物提供了前所未有的基因组资源。对这两个报春花物种的进化分析不仅揭示了更精确的分化时间，而且还为极端生境中发生的差异适应提供了一些新的见解。此外，我们还开发了两套遗传标记，单拷贝核基因和核微卫星（EST-SSR）。这两套标记都将有助于研究这个快速适应的分类群的遗传改良、种群遗传学和系统发育学。
