Open Access

ARTICLE

Chloroplast Genome Sequence Characterization and Phylogenetic Analysis of Pyrola Atropurpurea Franch

Wentao Sheng^*

Department of Biological Technology, Nanchang Normal University, Nanchang, 330032, China

* Corresponding Author: Wentao Sheng. Email:

(This article belongs to the Special Issue: Plant Genetic Diversity and Evolution)

Phyton-International Journal of Experimental Botany 2025, 94(2), 331-345. https://doi.org/10.32604/phyton.2025.061424

Received 24 November 2024; Accepted 14 January 2025; Issue published 06 March 2025

Abstract

Pyrola atropurpurea Franch is an important annual herbaceous plant. Few genomic analyses have been conducted on this plant, and chloroplast genome research will enrich its genomics basis. This study is based on high-throughput sequencing technology and Bioinformatics methods to obtain the sequence, structure, and other characteristics of the P. atropurpurea chloroplast genome. The result showed that the chloroplast genome of P. atropurpurea has a double-stranded circular structure with a total length of 172,535 bp and a typical four-segment structure. The genome has annotated a total of 132 functional genes, including 43 tRNAs, 8 rRNAs, 76 protein-coding genes, and 5 pseudo-genes. In total, 358 SSR loci were checked out, mainly composed of mononucleotide and trinucleotide repeat. There are three types of scattered repetitive sequences, totaling 4223, including 2452 forward repeats, 1763 palindrome repeats, and eight reverse repeats. The optimal codon usage frequency is relatively high with AT usage preference in this genome. Chloroplast genome comparative analysis in the family Ericaceae shows that the overall sequence is more complex, and there are more variations in the gene interval region. The collinearity analysis indicated that there is a complex rearrangement of species between different genera in Ericaceae. The selection pressure analysis showed that the protein-encoding genes rpl33 and rps16 were positively selected among the seven medicinal plants in Ericaceae. The maximum likelihood tree shows that the genetic relationship among P. atropurpurea, Pyrola rotundifolia, and Chimaphila japonica is relatively close. Therefore, an important data basis was provided for species identification, genetic diversity, and phylogenetic studies of P. atropurpurea and even this genus of plants.

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Supplementary Material

Supplementary Material File

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