Characterization of the complete chloroplast genome of Machilus cicatricosa and its phylogenetic relationships with related taxa

Gao Shang, Chen Qiaoyi, Cai Cuihua, Mo Luojian, Yao Gang, Huang Jiuxiang

Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 0

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南京林业大学学报（自然科学版）
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Journal of Nanjing Forestry University (Natural Sciences Edition） ›› 0 DOI: 10.12302/j.issn.1000-2006.202512013

Characterization of the complete chloroplast genome of Machilus cicatricosa and its phylogenetic relationships with related taxa

  • Gao Shang1, Chen Qiaoyi1, Cai Cuihua1, Mo Luojian2, Yao Gang1, Huang Jiuxiang1,*
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Abstract

[Objective] This study aimed to characterize the complete chloroplast (cp) genome of Machilus cicatricosa, a valuable timber species. We sought to identify hypervariable regions within the genus and elucidate its phylogenetic position within Machilus. This study provides a molecular basis for germplasm identification and phylogenetic reconstruction of the genus. [Method] The complete cp genome of M. cicatricosa was sequenced using genome skimming, followed by de novo assembly and functional annotation. Comparative genomic analyses and nucleotide diversity assessments were performed by integrating publicly available Machilus cp genome data from the NCBI database. Phylogenetic trees were constructed based on both complete cp genome sequences and concatenated hypervariable region matrices to evaluate the phylogenetic resolution of different datasets. [Result] The cp genome of M. cicatricosa is 152,651 bp in length, exhibiting a typical quadripartite structure and with 128 annotated genes. Intrageneric comparisons revealed a highly conserved genomic structure. Nucleotide diversity analysis identified several hypervariable regions, including ccsA-ndhD, trnH-psbA, and petA-psbJ. Phylogenetic analysis supported the division of Machilus into three major clades, with M. cicatricosa forming a strongly supported sister relationship with M. pomifera. Compared to the concatenated hypervariable regions, the phylogenetic tree based on the complete cp genome data demonstrated higher nodal support and a more stable topological structure. [Conclusion] The cp genome structure of M. cicatricosa is highly conserved within the genus. Our phylogenetic results do not support the traditional morphological classifications, suggesting that relevant morphological traits may have undergone parallel or convergent evolution. While the complete cp genome data significantly outperforms fragmentary data in resolving intrageneric relationships, support values for several internal branches remained insufficient. Future integration of additional nuclear genomic data will be essential to further clarify the evolutionary history and taxonomic framework of Machilus.

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Machilus cicatricosa / Machilus / chloroplast genome / phylogenetic analysis

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Gao Shang, Chen Qiaoyi, Cai Cuihua, Mo Luojian, Yao Gang, Huang Jiuxiang. Characterization of the complete chloroplast genome of Machilus cicatricosa and its phylogenetic relationships with related taxa[J]. Journal of Nanjing Forestry University (Natural Sciences Edition）. 0 https://doi.org/10.12302/j.issn.1000-2006.202512013

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