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Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes
Hu, Yuxin1,2; Xing, Weiyue1,2; Hu, Zhengyu3; Liu, Guoxiang1
2020
Source PublicationGENES
Volume11Issue:1Pages:12
Abstract

We sequenced the mitochondrial genome of six colonial volvocine algae, namely: Pandorina morum, Pandorina colemaniae, Volvulina compacta, Colemanosphaera angeleri, Colemanosphaera charkowiensi, and Yamagishiella unicocca. Previous studies have typically reconstructed the phylogenetic relationship between colonial volvocine algae based on chloroplast or nuclear genes. Here, we explore the validity of phylogenetic analysis based on mitochondrial protein-coding genes. We found phylogenetic incongruence of the genera Yamagishiella and Colemanosphaera. In Yamagishiella, the stochastic error and linkage group formed by the mitochondrial protein-coding genes prevent phylogenetic analyses from reflecting the true relationship. In Colemanosphaera, a different reconstruction approach revealed a different phylogenetic relationship. This incongruence may be because of the influence of biological factors, such as incomplete lineage sorting or horizontal gene transfer. We also analyzed the substitution rates in the mitochondrial and chloroplast genomes between colonial volvocine algae. Our results showed that all volvocine species showed significantly higher substitution rates for the mitochondrial genome compared with the chloroplast genome. The nonsynonymous substitution (dN)/synonymous substitution (dS) ratio is similar in the genomes of both organelles in most volvocine species, suggesting that the two counterparts are under a similar selection pressure. We also identified a few chloroplast protein-coding genes that showed high dN/dS ratios in some species, resulting in a significant dN/dS ratio difference between the mitochondrial and chloroplast genomes.

Keywordcolonial volvocine algae dN dS ratio mitochondrial genome phylogenetic analysis substitution rates
DOI10.3390/genes11010115
Indexed BySCI
Language英语
WOS Research AreaGenetics & Heredity
WOS SubjectGenetics & Heredity
WOS IDWOS:000514898000040
WOS KeywordMOLECULAR PHYLOGENY ; NUCLEAR GENOMES ; CHLOROPHYTA ; VOLVOCACEAE ; CHLOROPLAST ; MULTIPLE ; MORPHOLOGY ; EVOLUTION ; ALIGNMENT ; MODEL
PublisherMDPI
Citation statistics
Document Type期刊论文
Identifierhttp://ir.ihb.ac.cn/handle/342005/35109
Collection藻类生物技术和生物能源研发中心_期刊论文
Corresponding AuthorLiu, Guoxiang
Affiliation1.Chinese Acad Sci, Inst Hydrobiol, Key Lab Algal Biol, Wuhan 430072, Peoples R China
2.Univ Chinese Acad Sci, Sch Life Sci, Beijing 100049, Peoples R China
3.Chinese Acad Sci, Inst Hydrobiol, State Key Lab Freshwater Ecol & Biotechnol, Wuhan 430072, Peoples R China
Recommended Citation
GB/T 7714
Hu, Yuxin,Xing, Weiyue,Hu, Zhengyu,et al. Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes[J]. GENES,2020,11(1):12.
APA Hu, Yuxin,Xing, Weiyue,Hu, Zhengyu,&Liu, Guoxiang.(2020).Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes.GENES,11(1),12.
MLA Hu, Yuxin,et al."Phylogenetic Analysis and Substitution Rate Estimation of Colonial Volvocine Algae Based on Mitochondrial Genomes".GENES 11.1(2020):12.
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