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The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species

We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the fiv...

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Autores principales: Cheon, Kyeong-Sik, Kim, Kyung-Ah, Kwak, Myounghai, Lee, Byoungyoon, Yoo, Ki-Oug
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426196/
https://www.ncbi.nlm.nih.gov/pubmed/30893374
http://dx.doi.org/10.1371/journal.pone.0214162
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author Cheon, Kyeong-Sik
Kim, Kyung-Ah
Kwak, Myounghai
Lee, Byoungyoon
Yoo, Ki-Oug
author_facet Cheon, Kyeong-Sik
Kim, Kyung-Ah
Kwak, Myounghai
Lee, Byoungyoon
Yoo, Ki-Oug
author_sort Cheon, Kyeong-Sik
collection PubMed
description We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2–36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades.
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spelling pubmed-64261962019-04-02 The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species Cheon, Kyeong-Sik Kim, Kyung-Ah Kwak, Myounghai Lee, Byoungyoon Yoo, Ki-Oug PLoS One Research Article We report the complete chloroplast genomes of four Viola species (V. mirabilis, V. phalacrocarpa, V. raddeana, and V. websteri) and the results of a comparative analysis between these species and the published plastid genome of the congeneric species V. seoulensis. The total genome length of the five Viola species, including the four species analyzed in this study and the species analyzed in the previous study, ranged from 156,507 (V. seoulensis) to 158,162 bp (V. mirabilis). The overall GC contents of the genomes were almost identical (36.2–36.3%). The five Viola plastomes each contained 111 unique genes comprising 77 protein-coding genes, 30 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Among the annotated genes, 16 contained one or two introns. Based on the results of a chloroplast genome structure comparison using MAUVE, all five Viola plastomes were almost identical. Additionally, the large single copy (LSC), inverted repeat (IR), and small single copy (SSC) junction regions were conserved among the Viola species. A total of 259 exon, intron, and intergenic spacer (IGS) fragments were compared to verify the divergence hotspot regions. The nucleotide diversity (Pi) values ranged from 0 to 0.7544. The IR region was relatively more conserved than the LSC and SSC regions. The Pi values in ten noncoding regions were relatively high (>0.03). Among these regions, all but rps19-trnH, petG-trnW, rpl16-rps3, and rpl2-rpl23 represent useful molecular markers for phylogenetic studies and will be helpful to resolve the phylogenetic relationships of Viola. The phylogenetic tree, which used 76 protein-coding genes from 21 Malpighiales species and one outgroup species (Averrhoa carambola), revealed that Malpighiales is divided into five clades at the family level: Erythroxylaceae, Chrysobalanaceae, Euphorbiaceae, Salicaceae, and Violaceae. Additionally, Violaceae was monophyletic, with a bootstrap value of 100% and was divided into two subclades. Public Library of Science 2019-03-20 /pmc/articles/PMC6426196/ /pubmed/30893374 http://dx.doi.org/10.1371/journal.pone.0214162 Text en © 2019 Cheon et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Cheon, Kyeong-Sik
Kim, Kyung-Ah
Kwak, Myounghai
Lee, Byoungyoon
Yoo, Ki-Oug
The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title_full The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title_fullStr The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title_full_unstemmed The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title_short The complete chloroplast genome sequences of four Viola species (Violaceae) and comparative analyses with its congeneric species
title_sort complete chloroplast genome sequences of four viola species (violaceae) and comparative analyses with its congeneric species
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6426196/
https://www.ncbi.nlm.nih.gov/pubmed/30893374
http://dx.doi.org/10.1371/journal.pone.0214162
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