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

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.

Characterization and phylogenetic analysis of the complete mitochondrial genome sequence of Photinia serratifolia

“…The genus Photinia are evergreen plants that belongs to Rosaceae family, comprising approximately 60 species 1 . Photinia species are widely cultivated throughout the world and many are cultivated for gardening due to resistance to air pollution and other environmental stressors 2 , 3 .…”

“…The boundaries of some species have not been clearly defined in Rosaceae family due to similar morphological features exhibiting among Rosaceae species 1 . Compared with morphological identification, DNA sequences can produce more accurate phylogenetic relationships 1 , 6 .…”

“…The boundaries of some species have not been clearly defined in Rosaceae family due to similar morphological features exhibiting among Rosaceae species 1 . Compared with morphological identification, DNA sequences can produce more accurate phylogenetic relationships 1 , 6 . The phylogenetic study has greatly advanced the studies of taxonomic reclassification with the rapid advances in DNA technologies 7 , 8 .…”

“…Recently, the complete chloroplast genome sequences of Photinia × fraseri , Photinia davidsoniae , and Photinia glabra have been sequenced and published 1 , 27 , 28 . However, at present, no mitogenome of any species in Photinia has been reported.…”

“…It has been reported that the leaves of P. serratifolia contain essential oils, triterpenoids, flavonoids, polyphenols, and other bioactive compounds, which have been demonstrated to have antioxidant and anticancer activities in vitro 4,5 .The boundaries of some species have not been clearly defined in Rosaceae family due to similar morphological features exhibiting among Rosaceae species 1 . Compared with morphological identification, DNA sequences can produce more accurate phylogenetic relationships 1,6 . The phylogenetic study has greatly advanced the studies of taxonomic reclassification with the rapid advances in DNA technologies 7,8 .…”