Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum.
Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum.
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Tetrastigma hemsleyanum 比较转录组和全转录组合并分析的进化见解
DOI：
10.1186/s12870-018-1429-8
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发表时间：
2018-09-24
影响因子：
5.3
通讯作者：
Qiu Y
中科院分区：
文献类型：
--
作者：
Wang Y;Jiang W;Ye W;Fu C;Gitzendanner MA;Soltis PS;Soltis DE;Qiu Y
背景：三叶青具有重要的药用价值，并被用作东亚暖温带万年青（WTE）森林生物群落在新近纪时间尺度上进化历史的模式系统。然而，对T.雪胆属植物的研究目前受到缺乏基因组资源的阻碍。在这项研究中，我们从头组装和注释的两个cpDNA谱系（中东南与西南）的参考转录组。雪胆我们进一步使用比较基因组和多位点结合的方法来研究T。结果：共回收了52，838个和65，197个单一基因，N50分别为1，667和1，841 bp，分别用于中南-东南（CSE）和西南（SW）谱系，并在两个谱系之间鉴定了6，692个推定的直向同源物。对这些同源基因的Ka/Ks比值的估计显示，10个基因的Ka/Ks值显著大于0.5（P < 0.05），而2，099个（Ka/Ks< 0.5，P < 0.05）被推断为处于纯化选择中。基于三种生物信息学策略，我们从直系同源物中鉴定了总共1，018个单拷贝核基因（SCNG）。我们成功地设计了8对核基因引物，在一个亚群中进行了检测，结果表明，它们的种内变异很高（hT= 0.923，πT= 1.68×10-3）。hemsleyanum个体。与以前的cpDNA数据一致，大多数核基因位点构建的单倍型网络清楚地确定了这两个谱系。多位点合并分析表明，这两个谱系之间的分离似乎发生在上新世中期。尽管他们古老的分歧，这两个谱系经历了扩张，而本地化的规模，并继续交换基因在一个低rate.Conclusions：这项研究表明，转录组测序的实用程序作为基础，SCNG发展在非模式物种和优势，整合多个核基因座的地理和系统发育研究。
Background:Tetrastigma hemsleyanum is of great medicinal importance and used as a model system to address the evolutionary history of warm-temperate evergreen (WTE) forest biomes in East Asia over Neogene time scales. However, further studies on the neutral and adaptive divergence processes of T. hemsleyanum are currently impeded by a lack of genomic resources. In this study, we de novo assembled and annotated a reference transcriptome for two cpDNA lineages (Central-South-East vs. Southwest) of T. hemsleyanum. We further used comparative genomic and multilocus coalescent approaches to investigate the tempo and mode of lineage diversification in T. hemsleyanum.Results:A total of 52,838 and 65,197 unigenes with an N50 of 1,667 and 1,841 bp for Central-South-East (CSE) and Southwest (SW) lineages, respectively, were recovered, and 6,692 putative orthologs were identified between the two lineages. Estimation of Ka/Ksratios for these orthologs revealed that ten genes had Ka/Ksvalues significantly greater than 0.5 (P < 0.05), whereas 2,099 (Ka/Ks< 0.5, P < 0.05) were inferred to be under purifying selection. Based on three bioinformatic strategies, we identified a total of 1,018 single-copy nuclear genes (SCNGs) from the orthologs. We successfully designed eight nuclear gene primer pairs with high intraspecific variation (e.g. hT= 0.923, πT= 1.68×10-3), when surveyed across a subset of T. hemsleyanum individuals. Concordant with the previous cpDNA data, the haplotype networks constructed for most nuclear gene loci clearly identified the two lineages. A multilocus coalescence analysis suggested that the separation between the two lineages appears to have occurred during the mid-Pliocene. Despite their ancient divergence, both lineages experienced expansion at rather localized scales and have continued to exchange genes at a low rate.Conclusions:This study demonstrated the utility of transcriptome sequencing as a basis for SCNG development in non-model species and the advantages of integrating multiple nuclear loci for phylogeographic and phylogenetic studies.
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影响因子：
5.6
作者：
Goff SA;Vaughn M;McKay S;Lyons E;Stapleton AE;Gessler D;Matasci N;Wang L;Hanlon M;Lenards A;Muir A;Merchant N;Lowry S;Mock S;Helmke M;Kubach A;Narro M;Hopkins N;Micklos D;Hilgert U;Gonzales M;Jordan C;Skidmore E;Dooley R;Cazes J;McLay R;Lu Z;Pasternak S;Koesterke L;Piel WH;Grene R;Noutsos C;Gendler K;Feng X;Tang C;Lent M;Kim SJ;Kvilekval K;Manjunath BS;Tannen V;Stamatakis A;Sanderson M;Welch SM;Cranston KA;Soltis P;Soltis D;O'Meara B;Ane C;Brutnell T;Kleibenstein DJ;White JW;Leebens-Mack J;Donoghue MJ;Spalding EP;Vision TJ;Myers CR;Lowenthal D;Enquist BJ;Boyle B;Akoglu A;Andrews G;Ram S;Ware D;Stein L;Stanzione D
通讯作者：
Stanzione D
影响因子：
4
作者：
Feng Z;Hao W;Lin X;Fan D;Zhou J
通讯作者：
Zhou J
影响因子：
4.9
作者：
Clement, M;Posada, D;Crandall, KA
通讯作者：
Crandall, KA
影响因子：
5.7
作者：
Dai, Yajuan;Shen, Zonggen;Lu, Hongfei
通讯作者：
Lu, Hongfei
影响因子：
3.4
作者：
Duarte, Jill M.;Wall, P. Kerr;dePamphilis, Claude W.
通讯作者：
dePamphilis, Claude W.