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The complete chloroplast genome sequence of Photinia × fraseri, a medicinal plant and phylogenetic analysis.

ABSTRACT: Photinia × fraseri is a common ornamental arbor in the genus Photinia (family Rosaceae), which complete chloroplast (cp) genome was sequenced, assembled and annotated. The chloroplast genome of P. fraseri was 160,184 bp in length, including a large single copy (LSC) region of 88,121, a small single copy (SSC) region of 19,295 bp, and two inverted repeat (IR) regions of 26,384 bp. The GC contents of LSC, SSC, IR and whole genome are 36.5%, 34.1%, 30.3%, and 42.7%, respectively. There are 131 genes annotated, including 84 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. The phylogenetic analysis revealed that P. fraseri was most related to Photinia serratifolia as a sister group with 100% bootstrap support. The complete chloroplast genome sequences of P. fraseri will provide valuable genomic information to further illuminate phylogenetic classification of Photinia genus.

SUBMITTER: Li H

PROVIDER: S-EPMC8451673 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Sophora tonkinensis belongs to genus Sophora of the Fabaceae family. It is mainly distributed in the ridge and peak regions of limestone areas in western China and has high medicinal value and important ecological functions. Wild populations of S. tonkinensis are in danger and need urgent conservation. Furthermore, wild S. tonkinensis resources are very limited relative to the needs of the market, and many adulterants are present on the market. Therefore, a method for authenticating S. tonkinensis and its adulterants at the molecular level is needed. Chloroplast genomes are valuable sources of genetic markers for phylogenetic analyses, genetic diversity evaluation, and plant molecular identification. In this study, we report the complete chloroplast genome of S. tonkinensis. The circular complete chloroplast genome was 154,644 bp in length, containing an 85,810 bp long single-copy (LSC) region, an 18,321 bp short single-copy (SSC) region and two inverted repeat (IR) regions of 50,513 bp. The S. tonkinensis chloroplast genome comprised 129 genes, including 83 protein-coding genes, 38 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. The structure, gene order and guanine and cytosine (GC) content of the S. tonkinensis chloroplast genome were similar to those of the Sophora alopecuroides and Sophora flavescens chloroplast genomes. A total of 1,760 simple sequence repeats (SSRs) were identified in the chloroplast genome of S. tonkinensis, and most of them (93.1%) were mononucleotides. Moreover, the identified SSRs were mainly distributed in the LSC region, accounting for 60% of the total number of SSRs, while 316 (18%) and 383 (22%) were located in the SSC and IR regions, respectively. Only one complete copy of the rpl2 gene was present at the LSC/IRB boundary, while another copy was absent from the IRA region because of the incomplete structure caused by IR region expansion and contraction. The phylogenetic analysis placed S. tonkinensis in Papilionoideae, sister to S. flavescens, and the genera Sophora and Ammopiptanthus were closely related. The complete genome sequencing and chloroplast genome comparative analysis of S. tonkinensis and its closely related species presented in this paper will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

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The complete chloroplast genome sequence of Photinia × fraseri, a medicinal plant and phylogenetic analysis.

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