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Comparative Analysis of the Complete Mitochondrial Genome Sequence of an Alpine Plant Triosteum pinnatifidum

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Abstract—In this study, the complete mitochondrial genome (mt genome) of Triosteum pinnatifidum was investigated for the first time. The mt genome was consisted of 803 609 bp, comprised of 62 genes including 19 tRNA genes, 3 rRNA genes and 40 protein-coding genes. We detected protein-coding genes and codon usage, RNA editing sites and repeat sequences. The protein-coding genes substitution rates, DNA segments migration, comparison of six species genomic features were generated. Phylogenetic analysis of 32 species was also taken. A total of 463 RNA editing sites were found in 40 protein-coding genes. Being slightly positive, the GC-skew and AT-skew are 0.0060 and 0.0004, respectively. Most of PCGs have Ka/Ks ratio less than 1, indicating the existence of purifying or negative selection in these genes. This is the first report mt genome in the family Caprifoliaceae and could provide a useful foundation for evolutionary analysis, molecular biology and taxonomy in genus Triosteum and other higher plants.

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Funding

This research was funded by the CAS Light of West China Program (2022); Joint Grant from Chinese Academy of Science-People’s Government of Qinghai Province on Sanjiangyuan National Park, grant no. LHZX-2021-04.

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Authors and Affiliations

  1. State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810008, Xining, China

    Hairui Liu

  2. College of Eco-Environmental Engineering, Qinghai University, 810008, Xining, China

    Hairui Liu, Qingmeng Xiao, Quan Zhou, Xumin Li, Zhiwen Yao & Anqi Wang

  3. Department of Geological Engineering, Qinghai University, Xining, 810016, Qinghai, China

    Hairui Liu & Wenhui Liu

  4. Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810001, Qinghai, China

    Qingbo Gao & Shilong Chen

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  1. Hairui Liu
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Contributions

Conceptualization, H.R.L. and W.H.L.; methodology, Q.B.G. and Q.M.X; software, Q.M.X.; validation, S.L.C.; formal analysis, Q.M.X; investigation, H.R.L. and X.M.L.; resources, W.H.L.; data curation, X.M.L; writing—original draft preparation, Q.M.X; writing—review and editing, Q.M.X, Z.W.Y and Q.Z.; visualization, A.Q.W.; supervision, H.R.L. and Q.B.G.; project administration, H.R.L.; funding acquisition, H.R.L. All authors have read and agreed to the published version of the manuscript.

Corresponding authors

Correspondence to Qingbo Gao or Shilong Chen.

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COMPLIANCE WITH ETHICAL STANDARDS

The authors declare that they have no conflicts of interest. This article does not contain any studies involving animals or human participants performed by any of the authors.

DATA AVAILABILITY STATEMENT

The mitochondrial genome sequences of T. pinnatifidum were submitted to GenBank (MW526076).

Additional information

SUPPLEMENTARY MATERIALS

The following are available online at www.mdpi.com/xxx/s1, Table S1: Conversion of the RNA editing amino acids, Table S2: The Ka/Ks value of 19 protein-coding genes of Triosteum pinnatifidum vs. Actinidia arguta, Table S3: The Ka/Ks value of 24 protein-coding genes of Triosteum pinnatifidum versus Lactuca sativa, Table S4: The Ka/Ks value of 23 protein-coding genes of Triosteum pinnatifidum versus Hordeum vulgare, Table S5: The Ka/Ks value of 26 protein-coding genes of Triosteum pinnatifidum vs. Phoenix dactylifera, Table S6: The Ka/Ks value of 27 protein-coding genes of Triosteum pinnatifidum vs. Populus davidiana, Table S7: The Ka/Ks value of 27 protein-coding genes of Triosteum pinnatifidum vs. Senna occidentalis, Table S8: Information and GenBank accession number of the species used in genes comparison, Table S9: Gene features comparison of mt genome of six species.

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Liu, H., Liu, W., Xiao, Q. et al. Comparative Analysis of the Complete Mitochondrial Genome Sequence of an Alpine Plant Triosteum pinnatifidum. Cytol. Genet. 57, 335–346 (2023). https://doi.org/10.3103/S0095452723040084

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