Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights

Author:

Zhu Junqiao1ORCID,Huang Yang1ORCID,Chai Weiguo2,Xia Pengguo1ORCID

Affiliation:

1. College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China

2. Institute of Biotechnology, Hangzhou Academy of Agricultural Sciences, Hangzhou 310024, China

Abstract

Tetrastigma (Vitaceae) is known for its ornamental, medicinal, and ecological significance. However, the structural and variational characteristics of the Tetrastigma chloroplast genome and their impact on phylogenetic relationships remain underexplored. This study utilized bioinformatics methods to assemble and annotate the chloroplast genomes of 10 Tetrastigma species and compare them with five previously sequenced species. This study analyzed gene composition, simple sequence repeats, and codon usage patterns, revealing a high A/T content, uniquely identified pentanucleotide repeats in five species and several preferred codons. In addition, comparative analyses were conducted of the chloroplast genomes of 15 Tetrastigma species, examining their structural differences and identifying polymorphic hotspots (rps16, rps16-trnQ, trnS, trnD, psbC-trnS-psbZ, accD-psaI, psbE-petL-petG, etc.) suitable for DNA marker development. Furthermore, phylogenetic and selective pressure analyses were performed based on the chloroplast genomes of these 15 Tetrastigma species, validating and elucidating intra-genus relationships within Tetrastigma. Futhermore, several genes under positive selection, such as atpF and accD, were identified, shedding light on the adaptive evolution of Tetrastigma. Utilizing 40 Vitaceae species, the divergence time of Tetrastigma was estimated, clarifying the evolutionary relationships within Tetrastigma relative to other genera. The analysis revealed diverse divergences of Tetrastigma in the Miocene and Pliocene, with possible ancient divergence events before the Eocene. Furthermore, family-level selective pressure analysis identified key features distinguishing Tetrastigma from other genera, showing a higher degree of purifying selection. This research enriches the chloroplast genome data for Tetrastigma and offers new insights into species identification, phylogenetic analysis, and adaptive evolution, enhancing our understanding of the genetic diversity and evolutionary history of these species.

Funder

Zhejiang Provincial Natural Science Foundation of China

Zhejiang Province “Three agriculture nine side” agricultural science and technology cooperation program

Publisher

MDPI AG

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