The complete chloroplast genome of Photinia davidsoniae: molecular structures and comparative analysis

Jingling Li; Mei Jiang; Liqiang Wang; Jie Yu; Haimei Chen; Jingting Liu; Chang Liu

doi:10.1080/23802359.2021.1911698

The complete chloroplast genome of Photinia davidsoniae: molecular structures and comparative analysis

Mitochondrial DNA B Resour. 2021 Apr 19;6(4):1431-1439. doi: 10.1080/23802359.2021.1911698.

Authors

Jingling Li¹, Mei Jiang², Liqiang Wang², Jie Yu^{1

3}, Haimei Chen², Jingting Liu², Chang Liu²

Affiliations

¹ College of Horticulture and Landscape Architecture, Southwest University, Chongqing, China.
² Key Laboratory of Bioactive Substances and Resource Utilization of Chinese Herbal Medicine from Ministry of Education, Engineering Research Center of Chinese Medicine Resources from Ministry of Education, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
³ Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Chongqing, China.

Abstract

Photinia davidsoniae is a common ornamental arbor in the genus Photinia (family Rosaceae). Here, we sequenced and assembled the complete plastome of P. davidsoniae using the next-generation DNA sequencing technology. And we then compared it with nine Photinia species using a range of bioinformatics software tools. The ten plastomes had sizes ranging from 159,230 bp for P. beckii to 160,346 bp for P. davidsoniae. They all had a conservative quartile structure. It contained two single-copy regions: a large single-copy (LSC) region, a small single-copy (SSC) region, and a pair of inverted repeat (IR) regions. Each of the plastomes encoded 113 unique genes, including 79 protein-coding genes, four rRNA genes, and 30 tRNA genes. Furthermore, we detected six hypervariable regions (matK-rps16, rpoB-trnC, trnT-psbD, ndhC-trnV, psbE-petL, ndhF-rpl32-trnL), which could be used as potential molecular markers. We constructed two phylogenetic trees with plastomes or concatenated protein sequences of 25 species of 8 genera of Rosaceae. The tree constructed with complete plastomes has much stronger support. The results placed P. davidsoniae in the upper part of the phylogenetic tree. It shows that P. davidsoniae and P. lanuginosa are closely related. In summary, the plastomes of Photinia are conserved overall but carry significant minor variations, as expected. The results will be indispensable for distinguishing species, understanding the interspecific diversity, and elucidating the evolutionary processes of Photinia species.

Keywords: Photinia; chloroplast; comparative analysis; phylogenetic analysis; plastome.

Grants and funding

This research was funded by the National Natural Science Foundation of China [31772260]; Chongqing Study Abroad Innovation Project [cx2019052]; the Chinese Academy of Medical Sciences; the Innovation Funds for Medical Sciences (CIFMS) [2017-I2M-1-013, 2016-I2M-3-016]; the National Science Foundation Funds [81872966]; the National Science & Technology Fundamental Resources Investigation Program of China [2018FY100705]; and the National Mega-Project for Innovative Drugs of China [2019ZX09735-002].