ORIGINAL RESEARCH article
Front. Plant Sci.
Sec. Plant Systematics and Evolution
Comparative chloroplast genome analyses of Geum species: insights into genome characteristics, phylogenomic implications, and adaptive evolution
Provisionally accepted
- 1Inner Mongolia Normal University, Hohhot, China
- 2Smithsonian National Museum of Natural History, Washington, United States
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The genus Geum in the sense of Smedmark (2006) comprises about 72 species most frequently distributed in North America, Asia, and Europe, with a few representatives in South America, South Africa, Australia, and New Zealand. Previous phylogenetic analyses based on several molecular markers have contributed to the understanding of the delimitation of Geum, but the phylogenetic relationships within the group have not been resolved. Moreover, only a few chloroplast (cp) genomes of Geum species were reported, and no comparative cpchloroplast genome analyses among Geum species has been conducted to date, which is not conducive to gaining the understanding of its cpchloroplast genome evolution. This is the first study to conduct comparative genomic analyses on the cp genomes of 32 accessions of 11 Geum taxa. The Geum cp genomes showed a typical quadripartite structure like that of most other land plants, with a set of 129 genes including 84 protein-coding genes (PCGs), 37 transfer RNA (tRNA) genes, and eight ribosomal RNA (rRNA) genes. The Geum cp genomes were conserved in structure, size, GC contents, gene order and gene contents. Eleven highly variable regions (3′-trnK-UUU-matK, psbZ-trnG-GCC, trnR-UCU-atpA, petA-psbJ, 5′-trnK-UUU-rps16, rps16-trnQ-UUG, rpl32-trnL-UAG, ndhF-rpl32, trnS-GCU-trnG-UCC, ndhC-trnV-UAC, and petN-psbM) were considered as candidate molecular markers in the future studies on population genetics and systematic evolution of Geum species. The phylogenetic analyses provided new implications into the phylogenetic relationships among Geum species and supported Smedmark's recircumscription of Geum in a wide sense and corroborated the inclusion of Acomastylis, Coluria, and Taihangia in Geum. Twenty-three genes with positive selection sites were detected and adaptive evolution of these genes may play important roles in the adaptation of Geum species to their habitats. Overall, the present study enhanced our understanding of cp genome characteristics, phylogeny, and adaptive evolution of Geum species.
Keywords: Geum, Chloroplast genome, Comparative analyses, phylogeny, adaptive evolution
Received: 26 Sep 2025; Accepted: 13 Nov 2025.
Copyright: © 2025 Fu, Zhang, Guo, Wen and Li. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: QINQIN Li, liqq@imnu.edu.cn
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