Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis

Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and sp...

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Bibliographic Details
Published in:Journal of plant research 2024, Vol.137 (1), p.37-48
Main Authors: Xie, Junbo, Miao, Yujing, Zhang, Xinke, Zhang, Guoshuai, Guo, Baolin, Luo, Guangming, Huang, Linfang
Format: Article
Language:English
Subjects:
Adenine
Biomedical and Life Sciences
China
chloroplast genome
Chloroplasts
Chloroplasts - genetics
Evolution
Genes
Genome, Chloroplast - genetics
Genomes
Genomics
Genomics - methods
Geum - genetics
Geum aleppicum
Geum japonicum
Geum rupestre
Herbal medicine
herbal medicines
Life Sciences
phenotype
Phylogenetics
Phylogeny
Plant Biochemistry
Plant Ecology
Plant Physiology
Plant Sciences
Regular Paper – Taxonomy/Phylogenetics/Evolutionary Biology
rRNA
Thymine
tRNA
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Summary:Geum japonicum (Rosaceae) has been widely used in China as a traditional herbal medicine due to its high economic and medicinal value. However, the appearance of Geum species is relatively similar, making identification difficult by conventional phenotypic methods, and the studies of genomics and species evolution are lacking. To better distinguish the medicinal varieties and fill this gap, we carried out relevant research on the chloroplast genome of G. japonicum . Results show a typical quadripartite structure of the chloroplast genome of G. japonicum with a length of 156,042 bp. There are totally 131 unique genes in the genome, including 87 protein-coding genes, 36 tRNA genes, and 8 rRNA genes, and there were also 87 SSRs identified and mostly mononucleotide Adenine-Thymine. We next compared the plastid genomes among four Geum species and obtained 14 hypervariable regions, including ndh F, psb E, trn G-UCC, ccs A, trn Q-UUG, rps 16, psb K, trn L-UAA, ycf 1, ndh D, atp A, pet N, rps 14, and trn K-UUU. Phylogenetic analysis revealed that G. japonicum is most closely related to Geum aleppicum , and possibly has some evolutionary relatedness with an ancient relic plant Taihangia rupestris . This research enriched the genome resources and provided fundamental insights for evolutionary studies and the phylogeny of Geum .
ISSN:0918-9440
1618-0860
DOI:10.1007/s10265-023-01502-3