Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis

Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was de...

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Veröffentlicht in:PloS one 2019-07, Vol.14 (7), p.e0212325-e0212325
Hauptverfasser: Ye, Xuemin, Hu, Dongnan, Guo, Yangping, Sun, Rongxi
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Sun, Rongxi
description Castanopsis sclerophylla (Lindl.) Schott is an important species of evergreen broad-leaved tree in subtropical areas and has high ecological and economic value. However, there are few studies on its chloroplast genome. In this study, the complete chloroplast genome sequence of C. sclerophylla was determined using the Illumina HiSeq 2500 platform. The complete chloroplast genome of C. sclerophylla is 160,497 bp long, including a pair of inverted repeat (IR) regions (25,675 bp) separated by a large single-copy (LSC) region of 90,255 bp and a small single-copy (SSC) region of 18,892 bp. The overall GC content of the chloroplast genome is 36.82%. A total of 131 genes were found; of these, 111 genes are unique and annotated, including 79 protein-coding genes, 27 transfer RNA genes (tRNAs), and four ribosomal RNA genes (rRNAs). Twenty-one genes were found to be duplicated in the IR regions. Comparative analysis indicated that IR contraction might be the reason for the smaller chloroplast genome of C. sclerophylla compared to three congeneric species. Sequence analysis indicated that the LSC and SSC regions are more divergent than IR regions within Castanopsis; furthermore, greater divergence was found in noncoding regions than in coding regions. The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. Furthermore, these findings will be valuable for future studies of genetic diversity and enhance our understanding of the phylogenetic evolution of Castanopsis.
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The maximum likelihood phylogenetic analysis showed that four species of the genus Castanopsis form a monophyletic clade and that C. sclerophylla is closely related to Castanopsis hainanensis with strong bootstrap values. These results not only provide a basic understanding of Castanopsis chloroplast genomes, but also illuminate Castanopsis species evolution within the Fagaceae family. 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Schott: Genome structure and comparative and phylogenetic analysis</title><author>Ye, Xuemin ; Hu, Dongnan ; Guo, Yangping ; Sun, Rongxi</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c593t-2047cb4f5e95e5fd06b5adffcdd2a0990ed8fa9833d3a50aba952fcafb6cfa1e3</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2019</creationdate><topic>Amino acids</topic><topic>Analysis</topic><topic>Biodiversity</topic><topic>Biological evolution</topic><topic>Biology and Life Sciences</topic><topic>Castanopsis</topic><topic>Castanopsis sclerophylla</topic><topic>Chloroplasts</topic><topic>Chloroplasts - genetics</topic><topic>Chloroplasts - metabolism</topic><topic>Comparative analysis</topic><topic>Computer and Information Sciences</topic><topic>Contraction</topic><topic>Deoxyribonucleic acid</topic><topic>Divergence</topic><topic>DNA</topic><topic>Ecological monitoring</topic><topic>Engineering and Technology</topic><topic>Evolution</topic><topic>Fagaceae - genetics</topic><topic>Fagaceae - metabolism</topic><topic>Forestry</topic><topic>Future predictions</topic><topic>Genes</topic><topic>Genes, Plant</topic><topic>Genetic diversity</topic><topic>Genetic engineering</topic><topic>Genetic research</topic><topic>Genome, Chloroplast</topic><topic>Genomes</topic><topic>Genomics</topic><topic>Herbal medicine</topic><topic>Infrared analysis</topic><topic>Inverted repeat</topic><topic>Laboratories</topic><topic>Nucleotide sequence</topic><topic>Phylogenetics</topic><topic>Phylogeny</topic><topic>Plant sciences</topic><topic>Proteins</topic><topic>Ribonucleic acid</topic><topic>Ribosomal RNA</topic><topic>RNA</topic><topic>rRNA</topic><topic>Species</topic><topic>Transfer RNA</topic><topic>Trees</topic><topic>Whole Genome Sequencing</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Ye, Xuemin</creatorcontrib><creatorcontrib>Hu, Dongnan</creatorcontrib><creatorcontrib>Guo, Yangping</creatorcontrib><creatorcontrib>Sun, Rongxi</creatorcontrib><collection>Medline</collection><collection>MEDLINE</collection><collection>MEDLINE (Ovid)</collection><collection>MEDLINE</collection><collection>MEDLINE</collection><collection>PubMed</collection><collection>CrossRef</collection><collection>ProQuest Central (Corporate)</collection><collection>Animal Behavior Abstracts</collection><collection>Bacteriology Abstracts (Microbiology B)</collection><collection>Biotechnology Research Abstracts</collection><collection>Nursing &amp; 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subjects Amino acids
Analysis
Biodiversity
Biological evolution
Biology and Life Sciences
Castanopsis
Castanopsis sclerophylla
Chloroplasts
Chloroplasts - genetics
Chloroplasts - metabolism
Comparative analysis
Computer and Information Sciences
Contraction
Deoxyribonucleic acid
Divergence
DNA
Ecological monitoring
Engineering and Technology
Evolution
Fagaceae - genetics
Fagaceae - metabolism
Forestry
Future predictions
Genes
Genes, Plant
Genetic diversity
Genetic engineering
Genetic research
Genome, Chloroplast
Genomes
Genomics
Herbal medicine
Infrared analysis
Inverted repeat
Laboratories
Nucleotide sequence
Phylogenetics
Phylogeny
Plant sciences
Proteins
Ribonucleic acid
Ribosomal RNA
RNA
rRNA
Species
Transfer RNA
Trees
Whole Genome Sequencing
title Complete chloroplast genome of Castanopsis sclerophylla (Lindl.) Schott: Genome structure and comparative and phylogenetic analysis
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