Evolutionary insights from comparative transcriptome and transcriptome-wide coalescence analyses in Tetrastigma hemsleyanum

作者：Yihan Wang, Weimei Jiang, Wenqing Ye, Chengxin Fu, Matthew A. Gitzendanner, Pamela S. Soltis, Pamela S. Soltis, Yingxiong Qiu · 发表于：BMC Plant Biology · 年份：2018 · DOI：10.1186/s12870-018-1429-8 · 被引用次数：19 · 研究领域：Genomics and Phylogenetic Studies、Genetic diversity and population structure、Plant Diversity and Evolution

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. 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 K a / K s ratios for these orthologs revealed that ten genes had K a / K s values significantly greater than 0.5 ( P < 0.05), whereas 2,099 ( K a / K s < 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. h T = 0.923, π T = 1.68×10 -3 ), when surveyed across a subset of T. hemsleyanum individuals. Concordant with the previous cpDNA data, the haplotype ne...