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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.

SUBMITTER: Li J

PROVIDER: S-EPMC8078935 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Kaempferia galanga and Kaempferia elegans, which belong to the genus Kaempferia family Zingiberaceae, are used as valuable herbal medicine and ornamental plants, respectively. The chloroplast genomes have been used for molecular markers, species identification and phylogenetic studies. In this study, the complete chloroplast genome sequences of K. galanga and K. elegans are reported. Results show that the complete chloroplast genome of K. galanga is 163,811 bp long, having a quadripartite structure with large single copy (LSC) of 88,405 bp and a small single copy (SSC) of 15,812 bp separated by inverted repeats (IRs) of 29,797 bp. Similarly, the complete chloroplast genome of K. elegans is 163,555 bp long, having a quadripartite structure in which IRs of 29,773 bp length separates 88,020 bp of LSC and 15,989 bp of SSC. A total of 111 genes in K. galanga and 113 genes in K. elegans comprised 79 protein-coding genes and 4 ribosomal RNA (rRNA) genes, as well as 28 and 30 transfer RNA (tRNA) genes in K. galanga and K. elegans, respectively. The gene order, GC content and orientation of the two Kaempferia chloroplast genomes exhibited high similarity. The location and distribution of simple sequence repeats (SSRs) and long repeat sequences were determined. Eight highly variable regions between the two Kaempferia species were identified and 643 mutation events, including 536 single-nucleotide polymorphisms (SNPs) and 107 insertion/deletions (indels), were accurately located. Sequence divergences of the whole chloroplast genomes were calculated among related Zingiberaceae species. The phylogenetic analysis based on SNPs among eleven species strongly supported that K. galanga and K. elegans formed a cluster within Zingiberaceae. This study identified the unique characteristics of the entire K. galanga and K. elegans chloroplast genomes that contribute to our understanding of the chloroplast DNA evolution within Zingiberaceae species. It provides valuable information for phylogenetic analysis and species identification within genus Kaempferia.

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

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