Academic Journal
Chloroplast genome characterization and divergence time estimation of Persicaria capitata
| العنوان: | Chloroplast genome characterization and divergence time estimation of Persicaria capitata |
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| المؤلفون: | Zeng, Xianfa, Liu, Chang, Yang, Xiaoying, Wang, Xinyue, Luo, Jiangli, Zhou, Ying, Zhang, Liyan, Gao, Zengjie, Pu, Xiang |
| المصدر: | Acupuncture and Herbal Medicine ; ISSN 2765-8619 |
| بيانات النشر: | Ovid Technologies (Wolters Kluwer Health) |
| سنة النشر: | 2024 |
| الوصف: | Objective: With Persicaria capitata as test materials, we compared and analyzed the chloroplast genome characteristics as well as their phylogenetic relationships and evolutionary history with related species of Persicaria nepalensis , Persicaria japonica , Persicaria chinensis , Persicaria filiformis , Persicaria perfoliata , Persicaria pubescens , Persicaria hnydropiper. Methods: The Illumina HiSeq high-throughput sequencing platform was used for the first time for P. capitata chloroplast (cp) genome sequencing. NOVOPlasty and CpGAVAS2 were used for assembly and annotation, and Codon W, DnaSP, and MISA were used to conduct a series of comparative genomic analyses between the plant and seven species of the same genus. A phylogenetic tree was constructed using the maximum likelihood (ML) and neighbor-joining (NJ) methods, and divergence time was estimated using BEAST. Results: The total length of P. capitata cp genome was 158,821 bp, with a GC content of 38.0%, exhibiting a typical circular tetrad structure. The genome contains 127 annotated genes, including 82 protein-coding and 45 tRNA-encoding genes. The cp genome harbors single sequence repeat (SSR) loci primarily composed of A/T. The conserved species structure of this genus is reinforced by the expansion and contraction of the inverted repeat (IR) region. The non-coding regions of the cp genomes exhibited significant differences among the genera. Six different mutation hotspots ( psbK - psbI , atpI - rps2 , petN - psbD , atpB - rbcL , cemA - petA , ndhI - ndhA - ycf1 ) were screened from the non-coding regions of genes with high nucleotide variability (pI). These hotspots were expected to define the phylogenetic species of Persicaria . Furthermore, phylogenetic analysis of Polygonaceae plants showed that P. capitata was more closely related to P. chinensis than P. nepalensis . Analysis of divergence time indicated that Polygonaceae originated in the Late Cretaceous (~180 Ma) and began to differentiate during the Middle Miocene. Persicaria differentiated ... |
| نوع الوثيقة: | article in journal/newspaper |
| اللغة: | English |
| DOI: | 10.1097/hm9.0000000000000133 |
| DOI: | 10.1097/HM9.0000000000000133 |
| الاتاحة: | https://doi.org/10.1097/hm9.0000000000000133 https://journals.lww.com/10.1097/HM9.0000000000000133 |
| Rights: | http://creativecommons.org/licenses/by-nc-nd/4.0/ |
| رقم الانضمام: | edsbas.5A6268E0 |
| قاعدة البيانات: | BASE |
| DOI: | 10.1097/hm9.0000000000000133 |
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