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

Abstract

BackgroundTetrastigma 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.ResultsA 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/Ks ratios for these orthologs revealed that ten genes had Ka/Ks values 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.ConclusionsThis 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.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1429-8) contains supplementary material, which is available to authorized users.

Seasonal Variation in Transcriptomic Profiling of Tetrastigma hemsleyanum Fully Developed Tuberous Roots Enriches Candidate Genes in Essential Metabolic Pathways and Phytohormone Signaling

“…When blasted against the NR database by using BLASTx, 74.23% of the unigenes matched to the sequences of Vitis vinifera, followed by Anthurium amnicola, Theobroma cacao, barley, and other species (Supplementary Figure 1D), the observed high-level matching of SYQ and grapes was expected because both species belong to the same family Vitaceae, and are in near-evolutional relation with each other (Wang Y. H. et al, 2015). Similar results were observed in two lineages of T. hemsleyanum Central-South-East (CSE) 92.44% and Southwest (SW) 89.62%, separately (Wang et al, 2018). These two lineages are classified by using the chloroplast DNA (Wang Y. H. et al, 2015).…”

“…RNA-Seq is also a powerful tool to study the biosynthesis pathways of secondary metabolites in TRs and tubers (Wang et al, 2017;Wu et al, 2017) such as flavonoids and phenylpropanoids (FPs) in Pueraria lobata (Wang et al, 2015b); saponin in Panax (Rai et al, 2016;Lee et al, 2017); and alkaloids in Corydalis yanhusuo (Liao et al, 2016). Wang Y. H. et al (2015) and Wang et al (2018) used RNA-Seq and chloroplast DNA sequencing to integrate multiple nuclear loci for phylogeographic and phylogenetic diversities of SYQ populations. Peng et al (2019Peng et al ( , 2020 studied the transcriptome, endogenous hormones, and unigenes in flavonoid biosynthesis in SYQ leaves in response to short-time cold while Yan et al (2020) summarized the integration of transcriptome and metabolome of SYQ purple and green leaves and discussed the expression patterns of some genes in the anthocyanin biosynthesis pathway.…”

Complete chloroplast genome sequence and phylogenetic analysis of wasabi (Eutrema japonicum) and its relatives

“…*The observed mutation rates increase significantly (homopolymer) when mononucleotide.repeat numbers reach or exceed 9 bp 16 .…”

“…This discrepancy is probably due to the previous single matK gene analysis overestimating the divergence time. Divergence dates estimated from single gene phylogenetic trees can lead to overestimates of divergence times because gene divergence inevitably predates speciation 15,16 . Our present genome sequence data using many genes has provided more informative data.…”

Physiological Responses of the Tetrastigma hemsleyanum Plant under Different Color Films

“…Tetrastigma hemsleyanum is a precious plant in China (Wang et al, 2018a), It is known for its anti-inflammatory, antioxidant, and antitumor activities (Chen et al, 2017;Wang et al, 2017;Zhu et al, 2020) in Chinese herbology. Wu et al (2019) reported that the flavonoids present in T. hemsleyanum have a noticeable antitumor effect in leukemia and colon cancer.…”