Comparative plastomes of species from Phrymaceae and Mazaceae: insights into adaptive evolution, codon usage bias, and phylogenetic relationships.

IF 2.3 3区 生物学 Q3 BIOTECHNOLOGY & APPLIED MICROBIOLOGY
Genome Pub Date : 2023-11-01 Epub Date: 2023-05-09 DOI:10.1139/gen-2023-0014
Xiaofeng Chi, Ronglian Chen, Faqi Zhang, Shilong Chen
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引用次数: 0

Abstract

The phylogeny of the species from Phrymaceae and Mazaceae has undergone many adjustments and changes in recent years. Moreover, there is little plastome information on the Phrymaceae. In this study, we compared the plastomes of six species from the Phrymaceae and 10 species from the Mazaceae. The gene order, contents, and orientation of the 16 plastomes were found to be highly similar. A total of 13 highly variable regions were identified among the 16 species. An accelerated rate of substitution was found in the protein-coding genes, particularly cemA and matK. The combination of effective number of codons, parity rule 2, and neutrality plots revealed that the codon usage bias is affected by mutation and selection. The phylogenetic analysis strongly supported {Mazaceae [(Phrymaceae + Wightiaceae) + (Paulowniaceae + Orobanchaceae)]} relationships in the Lamiales. Our findings can provide useful information to analyze the phylogeny and molecular evolution within the Phrymaceae and Mazaceae.

Phrymaceae和Mazaceae物种的比较质体:对适应性进化、密码子使用偏差和系统发育关系的见解。
近年来,该属植物的系统发育经历了许多调整和变化。此外,关于Phrymaceae的质体信息很少。在本研究中,我们比较了6种水草科植物和10种马祖科植物的质体。发现16个质体的基因顺序、含量和取向高度相似。在16个物种中,共鉴定出13个高度可变区域。在蛋白质编码基因中发现了加速的取代率,特别是cemA和matK。密码子的有效数量、奇偶校验规则2和中性图的组合表明,密码子的使用偏差受到突变和选择的影响。系统发育分析有力地支持了Lamiales中的{Mazaceae[(Phrymaceae+Wightiaceae)+(泡桐科+Orobancheae)]}关系。我们的发现可以为分析Phrymaceae和Mazaceae的系统发育和分子进化提供有用的信息。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Genome
Genome 生物-生物工程与应用微生物
CiteScore
5.30
自引率
3.20%
发文量
42
审稿时长
6-12 weeks
期刊介绍: Genome is a monthly journal, established in 1959, that publishes original research articles, reviews, mini-reviews, current opinions, and commentaries. Areas of interest include general genetics and genomics, cytogenetics, molecular and evolutionary genetics, developmental genetics, population genetics, phylogenomics, molecular identification, as well as emerging areas such as ecological, comparative, and functional genomics.
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