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

Area of Science:

• Genomics
• Evolutionary Biology
• Bioinformatics

Background:

• Tetrastigma hemsleyanum holds significant medicinal value and serves as a model for East Asian warm-temperate evergreen forest biome evolution.
• Genomic resources are crucial for studying neutral and adaptive divergence processes in T. hemsleyanum.

Purpose of the Study:

• To de novo assemble and annotate a reference transcriptome for two cpDNA lineages of T. hemsleyanum.
• To investigate lineage diversification using comparative genomics and multilocus coalescent approaches.

Main Methods:

• Transcriptome sequencing and de novo assembly for two T. hemsleyanum lineages (Central-South-East and Southwest).
• Comparative genomic analysis to identify orthologs and estimate selection pressures (Ka/Ks ratios).
• Multilocus coalescent and phylogenetic analyses using identified single-copy nuclear genes (SCNGs).

Main Results:

• Assembly of 52,838 and 65,197 unigenes, identification of 6,692 orthologs between lineages.
• Identification of genes under selection and 1,018 single-copy nuclear genes (SCNGs).
• Evidence for mid-Pliocene divergence between lineages, localized expansion, and low-level gene flow.

Conclusions:

• Transcriptome sequencing is effective for SCNG development in non-model organisms.
• Integrating multiple nuclear loci enhances phylogeographic and phylogenetic resolution.