Comparative transcriptome analysis and marker development of two closely related Primrose species (Primula poissonii and Primula wilsonii).
Comparative transcriptome analysis and marker development of two closely related Primrose species (Primula poissonii and Primula wilsonii).
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两个密切相关的报春花物种（普氏报春花和威尔逊报春花）的比较转录组分析和标记开发
DOI：
10.1186/1471-2164-14-329
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发表时间：
2013-05-14
期刊：
影响因子：
4.4
通讯作者：
Ge XJ
中科院分区：
文献类型：
--
作者：
Zhang L;Yan HF;Wu W;Yu H;Ge XJ
背景
报春花是中国西部东喜马拉雅-横断山区重要的早春园林植物，具有多样性和物种多样性中心。由于缺乏基因组资源，报春花属的种群遗传学、物种形成和系统发育的研究一直受到阻碍。在本研究中，我们在Illumina Genome Analyzer平台上使用短读数对两个近缘关系密切的报春花物种--报春花和报春花的转录进行了测序。
结果
我们获得了55,284和55,011个重叠群，N50值分别为938和1,085，并在这两个物种之间鉴定出6654对推定的同源基因。对这些同源基因的非同义/同义替换率的估计表明，877对同源基因可能处于正选择状态(Ka/Ks 0.5)，功能浓缩分析表明，相当大比例的直系基因属于DNA修复和抗逆性类别，这可能为这两个密切相关的报春花属植物如何以不同的方式适应极端环境提供一些线索。首次能够估计辐射物种对P.poissonii和P.wilsonii之间的分歧时间；这被发现大约为0.90±0.57 Mya，位于中更新世的多瑙冰川和冈兹冰川之间。根据报春花属和报春花属植物之间54对同源SSR序列，设计并验证了该两种报春花属植物的SSR序列。这些配对中约有一半成功地为两个物种扩增。在4种模式植物共有的959个单拷贝核基因(称为APVO基因)中，111个单拷贝核基因被证实存在于报春花属物种中，并设计了外显子锚定和内含子跨越的引物。
结论
我们鉴定了这两个报春花物种的转录本，并为这些重要的园林植物产生了前所未有的数量的基因组资源。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，还为在极端生境中如何发生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，即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种快速适应的分类群的遗传改良、种群遗传学和系统发育。
Background
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.
Results
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.
Conclusion
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.
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影响因子：
4.4
作者：
Logacheva MD;Kasianov AS;Vinogradov DV;Samigullin TH;Gelfand MS;Makeev VJ;Penin AA
通讯作者：
Penin AA
影响因子：
64.8
作者：
Jaillon, Olivier;Aury, Jean-Marc;Wincker, Patrick
通讯作者：
Wincker, Patrick
影响因子：
3.4
作者：
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通讯作者：
dePamphilis, Claude W.
影响因子：
7.3
作者：
Li, Li-Juan;Ren, Fei;Wang, Xue-Chen
通讯作者：
Wang, Xue-Chen
影响因子：
64.8
作者：
Bustamante, CD;Fledel-Alon, A;Clark, AG
通讯作者：
Clark, AG