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Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications
Tang, J.; Zou, R.; Chen, T.; Pan, L.; Zhu, S.; Ding, T.; Chai, S.; Wei, X. Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Forests2023, 14, 2069.
Tang, J.; Zou, R.; Chen, T.; Pan, L.; Zhu, S.; Ding, T.; Chai, S.; Wei, X. Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Forests 2023, 14, 2069.
Tang, J.; Zou, R.; Chen, T.; Pan, L.; Zhu, S.; Ding, T.; Chai, S.; Wei, X. Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Forests2023, 14, 2069.
Tang, J.; Zou, R.; Chen, T.; Pan, L.; Zhu, S.; Ding, T.; Chai, S.; Wei, X. Comparative Analysis of the Complete Chloroplast Genomes of Six Endangered Cycas Species: Genomic Features, Comparative Analysis, and Phylogenetic Implications. Forests 2023, 14, 2069.
Abstract
Cycas (family Cycadaceae), spread throughout tropical and subtropical regions, is crucial in con-servation biology. Due to the subtle morphological variations between species, a solid spe-cies-level phylogeny for Cycas is lacking. Because of the rapid progress in high-throughput se-quencing technology, it has become feasible to acquire complete chloroplast (cp) genome se-quences, which provide a molecular foundation for phylogenetic research. In the present study, we employed next-generation sequencing technology to assemble and analyze the chloroplast genomes of six Cycas plants, including their genome structure, GC content, and nucleotide di-versity. The Cycas chloroplast genome spans 162,038 to 162,159 bp and contains 131 genes, in-cluding 86 protein-coding genes, 37 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Through a comparative analysis, we found that the chloroplast genome of Cycas was highly conserved, as indicated by the contraction and expansion of the inverted repeat (IR) re-gions and sequence polymorphisms. In addition, several non-coding sites (psbK-psbI, petN-psbM, trnE-UUC-psbD, ndhC-trnM-CAU, and rpl32-trnP-GGG) showed significant varia-tion. The utilization of phylogenetic analysis relying on protein-coding genes has substantiated the division of Cycas primarily into four groups. The application of these findings will prove valuable in evaluating genetic diversity and the phylogenetic connections among closely related species. Moreover, it will provide essential support for the advancement of wild germplasm re-sources.
Keywords
Cycas; chloroplast genome; phylogenetic analysis; SSR; large repeats
Subject
Biology and Life Sciences, Biochemistry and Molecular Biology
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
