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Open AccessArticle
Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights
by
Junqiao Zhu
Junqiao Zhu 1
,
Yang Huang
Yang Huang 1
,
Weiguo Chai
Weiguo Chai 2 and
Pengguo Xia
Pengguo Xia 1,*
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
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2024, 25(15), 8290; https://doi.org/10.3390/ijms25158290 (registering DOI)
Submission received: 25 May 2024
/
Revised: 26 July 2024
/
Accepted: 26 July 2024
/
Published: 29 July 2024
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.
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MDPI and ACS Style
Zhu, J.; Huang, Y.; Chai, W.; Xia, P.
Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights. Int. J. Mol. Sci. 2024, 25, 8290.
https://doi.org/10.3390/ijms25158290
AMA Style
Zhu J, Huang Y, Chai W, Xia P.
Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights. International Journal of Molecular Sciences. 2024; 25(15):8290.
https://doi.org/10.3390/ijms25158290
Chicago/Turabian Style
Zhu, Junqiao, Yang Huang, Weiguo Chai, and Pengguo Xia.
2024. "Decoding the Chloroplast Genome of Tetrastigma (Vitaceae): Variations and Phylogenetic Selection Insights" International Journal of Molecular Sciences 25, no. 15: 8290.
https://doi.org/10.3390/ijms25158290
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