PJB-2023-360
The complete chloroplast genome and phylogeny of Euphorbia altotibetica (Euphorbiaceae), an endemic medicinal plant species from northwest China
Rongju Qu, Xuanrui Mao, Yonghui Zhou, Yuping Liu, Xu Su, Xiayu Hu, Ping Yang, Changyuan Zheng and Aftab Ahmad
Abstract
Euphorbia altotibetica is an endemic medicinal herb species to Northwest China, belonging to genus Euphorbia of Euphorbiaceae. We sequenced and assembled the complete chloroplast genome of Euphorbia altotibetica followed by annotation using high-throughput sequencing technology, and annotation pipelines. Our result shows that the complete chloroplast genome of E. altotibetica is 161,141 bp in length with a GC content of 35.5%, with a typical tetrad ring structure. The chloroplast assembly consists of a large single copy region, a small single copy region, and two inverted repeat regions, with size 89,398 bp, 17,802bp, and 26,133 bp respectively. A total of 130 genes were annotated, including eight rRNA genes, 38 tRNA genes, and 84 protein genes. We also detected 90 simple sequence repeats (SSRs) loci in the chloroplast genome, which are mainly composed of mononucleotide repeats. Codon bias analysis showed that isoleucine (Ile) is the most abundant amino acid with frequency (8.78%), and four codons (ycf1, ycf2, rpl20, and rpl22) have the relative synonymous codon usage (RSCU) value above one. In the IRa regions of E. altotibetica, there is deletion in gene rps19. Phylogenetic analysis based on the chloroplast genome of E. altotibetica along with 68 other species of genus Euphorbia showed that the E. altotibetica and E. peplus were closest relatives, and nested together with a support rate of 100%. In this study, we obtained and characterized the complete chloroplast genome of E. altotibetica followed by its phylogenetic analysis for the first time. Our study provides theoretical basis for future research to understand the genetic diversity, phylogeny, population genetic structure, and speciation mechanism of genus Euphorbiaceae
To Cite this article:
Qu, R., X. Mao, Y. Zhou, Y. Liu, X. Su, X. Hu, P. Yang, C. Zheng and A. Ahmad. 2025. The complete chloroplast genome and phylogeny of Euphorbia altotibetica (Euphorbiaceae), an endemic medicinal plant species from northwest China. Pak. J. Bot., 57(2): DOI: http://dx.doi.org/10.30848/PJB2025-2(33)
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