Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae
In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectiv...
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doaj-5c1a40aef471464bb9b72db3493d77ed2021-02-11T07:21:58ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-02-011110.3389/fpls.2020.593984593984Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within CelastrineaeYongtan Li0Yongtan Li1Yan Dong2Yan Dong3Yichao Liu4Yichao Liu5Yichao Liu6Xiaoyue Yu7Xiaoyue Yu8Minsheng Yang9Minsheng Yang10Yinran Huang11Forest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaInstitute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaForest Department, Forestry College, Hebei Agricultural University, Baoding, ChinaHebei Key Laboratory for Tree Genetic Resources and Forest Protection, Baoding, ChinaInstitute of Landscaping, Hebei Academic of Forestry and Grassland, Shijiazhuang, ChinaIn this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species.https://www.frontiersin.org/articles/10.3389/fpls.2020.593984/fullEuonymuschloroplast genomeadaptive evolutionmolecular markerphylograms |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Yongtan Li Yongtan Li Yan Dong Yan Dong Yichao Liu Yichao Liu Yichao Liu Xiaoyue Yu Xiaoyue Yu Minsheng Yang Minsheng Yang Yinran Huang |
spellingShingle |
Yongtan Li Yongtan Li Yan Dong Yan Dong Yichao Liu Yichao Liu Yichao Liu Xiaoyue Yu Xiaoyue Yu Minsheng Yang Minsheng Yang Yinran Huang Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae Frontiers in Plant Science Euonymus chloroplast genome adaptive evolution molecular marker phylograms |
author_facet |
Yongtan Li Yongtan Li Yan Dong Yan Dong Yichao Liu Yichao Liu Yichao Liu Xiaoyue Yu Xiaoyue Yu Minsheng Yang Minsheng Yang Yinran Huang |
author_sort |
Yongtan Li |
title |
Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae |
title_short |
Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae |
title_full |
Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae |
title_fullStr |
Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae |
title_full_unstemmed |
Comparative Analyses of Euonymus Chloroplast Genomes: Genetic Structure, Screening for Loci With Suitable Polymorphism, Positive Selection Genes, and Phylogenetic Relationships Within Celastrineae |
title_sort |
comparative analyses of euonymus chloroplast genomes: genetic structure, screening for loci with suitable polymorphism, positive selection genes, and phylogenetic relationships within celastrineae |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2021-02-01 |
description |
In this study, we assembled and annotated the chloroplast (cp) genome of the Euonymus species Euonymus fortunei, Euonymus phellomanus, and Euonymus maackii, and performed a series of analyses to investigate gene structure, GC content, sequence alignment, and nucleic acid diversity, with the objectives of identifying positive selection genes and understanding evolutionary relationships. The results indicated that the Euonymus cp genome was 156,860–157,611bp in length and exhibited a typical circular tetrad structure. Similar to the majority of angiosperm chloroplast genomes, the results yielded a large single-copy region (LSC) (85,826–86,299bp) and a small single-copy region (SSC) (18,319–18,536bp), separated by a pair of sequences (IRA and IRB; 26,341–26,700bp) with the same encoding but in opposite directions. The chloroplast genome was annotated to 130–131 genes, including 85–86 protein coding genes, 37 tRNA genes, and eight rRNA genes, with GC contents of 37.26–37.31%. The GC content was variable among regions and was highest in the inverted repeat (IR) region. The IR boundary of Euonymus happened expanding resulting that the rps19 entered into IR region and doubled completely. Such fluctuations at the border positions might be helpful in determining evolutionary relationships among Euonymus. The simple-sequence repeats (SSRs) of Euonymus species were composed primarily of single nucleotides (A)n and (T)n, and were mostly 10–12bp in length, with an obvious A/T bias. We identified several loci with suitable polymorphism with the potential use as molecular markers for inferring the phylogeny within the genus Euonymus. Signatures of positive selection were seen in rpoB protein encoding genes. Based on data from the whole chloroplast genome, common single copy genes, and the LSC, SSC, and IR regions, we constructed an evolutionary tree of Euonymus and related species, the results of which were consistent with traditional taxonomic classifications. It showed that E. fortunei sister to the Euonymus japonicus, whereby E. maackii appeared as sister to Euonymus hamiltonianus. Our study provides important genetic information to support further investigations into the phylogenetic development and adaptive evolution of Euonymus species. |
topic |
Euonymus chloroplast genome adaptive evolution molecular marker phylograms |
url |
https://www.frontiersin.org/articles/10.3389/fpls.2020.593984/full |
work_keys_str_mv |
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