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Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating

Citation

Li, Qin-Qin; Zhang, Guo-Jian; Zhang, Zhi-Ping (2022), Comparative analysis of chloroplast genomes of Sanguisorba species and insights into phylogenetic implications and molecular dating, Dryad, Dataset, https://doi.org/10.5061/dryad.n5tb2rbzr

Abstract

Sanguisorba is a small genus, which consists of about 15 species widely distributed in North America and Eurasia. Previous studies on Sanguisorba are useful for understanding of phylogeny and chloroplast (cp) genome evolution of Sanguisorba. However, the cp genome resources of Sanguisorba are still limited, and the phylogeny and molecular dating for Sanguisorba and its relatives still need further explored. Here, we reported four cp genomes of Sanguisorba and conducted comparative analysis of the four Sanguisorba cp genomes plus five previously published ones. The nine cp genomes of Sanguisorba have typical tetrad quadripartite structure, with a total length of 154 282 to 155 730 bp, and their gene content, gene structure, and gene order are relatively conservative. The analysis of single copy (SC)/inverted repeat (IR) boundaries shows very slight boundary differences in Sanguisorba cp genomes. Eight variation hotspots were screened as excellent candidate markers of Sanguisorba. Phylogenetic analysis indicated Sanguisorba was monophyletic and was a member of tribe Agrimonieae subtribe Sanguisorbinae. Within Sanguisorba, S. filiformis is a sister group of six other taxa in the present sampling. Estimation of the divergence times indicated that subtribes Agrimoniinae and Sanguisorbinae diverged at the transition between the Oligocene and the Miocene, and divergent times of Agrimonieae genera ranged from the late Miocene to the Middle Pleistocene. This study enriches the available cp genome resources of Sanguisorba, and it is of great significance to further study the phylogeny and evolution of Sanguisorba and its relatives.

Usage Notes

Table S1. The GenBank accession numbers of all the 36 chloroplast genome sequences used for phylogenetic analysis.

Table S2. The nucleotide diversity (Pi) values of 264 homologous loci.

Data_matrix. Data matrix used for phylogenetic analysis and molecular dating.

Funding

National Natural Science Foundation of China, Award: 31460051

Natural Science Foundation of Inner Mongolia, Award: 2022LHQN03004