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

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Abstract

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 ndhF, psbE, trnG-UCC, ccsA, trnQ-UUG, rps16, psbK, trnL-UAA, ycf1, ndhD, atpA, petN, rps14, and trnK-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.

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Funding

This research was funded by the CAMS Innovation Fund for Medical Sciences (CIFMS, 2022-I2M-1-017), the National Natural Science Foundation of China (U1812403-1, 82073960 and 82274045), the Open Fund of State Key Laboratory of Southwestern Chinese Medicine Resources (SKLTCM2022015), and National Science & Technology Fundamental Resources Investigation Program of China (2018FY100701), which are gratefully acknowledged. We sincerely appreciate the support provided by the above funds.

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  1. Key Laboratory of Chinese Medicine Resources Conservation, Institute of Medicinal Plant Development, State Administration of Traditional Chinese Medicine of China, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, 100193, China

    Junbo Xie, Yujing Miao, Xinke Zhang, Guoshuai Zhang, Baolin Guo & Linfang Huang

  2. School of Pharmacy, Jiangxi University of Chinese Medicine, Nanchang, 330000, China

    Junbo Xie & Guangming Luo

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  1. Junbo Xie
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Xie, J., Miao, Y., Zhang, X. et al. Comparative complete chloroplast genome of Geum japonicum: evolution and phylogenetic analysis. J Plant Res 137, 37–48 (2024). https://doi.org/10.1007/s10265-023-01502-3

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