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Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields

Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we a...

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Autores principales: Gao, Yuan, Shen, Guohui, Yuan, Guohui, Tian, Zhihui
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698722/
https://www.ncbi.nlm.nih.gov/pubmed/36430336
http://dx.doi.org/10.3390/ijms232213864
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author Gao, Yuan
Shen, Guohui
Yuan, Guohui
Tian, Zhihui
author_facet Gao, Yuan
Shen, Guohui
Yuan, Guohui
Tian, Zhihui
author_sort Gao, Yuan
collection PubMed
description Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution.
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spelling pubmed-96987222022-11-26 Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields Gao, Yuan Shen, Guohui Yuan, Guohui Tian, Zhihui Int J Mol Sci Article Echinochloa crus-galli var. crus-galli, E. crus-galli var. zelayensis, and E. glabrescens, morphologically similar at the seedling stage, are the most pernicious barnyard grass species in paddy fields worldwide. Chloroplast (cp) genomes could be conducive to their identification. In this study, we assembled the complete cp genome sequences of Echinochloa crus-galli var. crus-galli (139,856 bp), E. crus-galli var. zelayensis (139,874 bp), and E. glabrescens (139,874 bp), which exhibited a typical circular tetramerous structure, large and small single-copy regions, and a pair of inverted repeats. In Echinochloa crus-galli var. crus-galli, there were 136 simple sequence (SSRs) and 62 long (LRs) repeats, and in the other two species, 139 SSRs and 68 LRs. Each cp genome contains 92 protein-encoding genes. In Echinochloa crus-galli var. crus-galli and E. glabrescens, 321 and 1 single-nucleotide polymorphisms were detected compared to Echinochloa crus-galli var. zelayensis. IR expansion and contraction revealed small differences between the three species. The phylogenetic tree based on cp genomes demonstrated the phylogenetic relationship between ten barnyard grass species and other common Gramineae plants, showing new genetic relationships of the genus Echinochloa. This study provides valuable information on cp genomes, useful for identifying and classifying the genus Echinochloa and studying its phylogenetic relationships and evolution. MDPI 2022-11-10 /pmc/articles/PMC9698722/ /pubmed/36430336 http://dx.doi.org/10.3390/ijms232213864 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Gao, Yuan
Shen, Guohui
Yuan, Guohui
Tian, Zhihui
Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title_full Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title_fullStr Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title_full_unstemmed Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title_short Comparative Analysis of Whole Chloroplast Genomes of Three Common Species of Echinochloa (Gramineae) in Paddy Fields
title_sort comparative analysis of whole chloroplast genomes of three common species of echinochloa (gramineae) in paddy fields
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9698722/
https://www.ncbi.nlm.nih.gov/pubmed/36430336
http://dx.doi.org/10.3390/ijms232213864
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