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Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)

Eragrostis of the tribe Eragrostideae is a taxonomically complex genus, because of its polyploid nature and the presence of similar morphological characters among its species. However, the relationship between these morphologically indistinguishable species at the genomic level has not yet been inve...

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Autores principales: Somaratne, Yamuna, Guan, De-Long, Abbood, Nibras Najm, Zhao, Liang, Wang, Wen-Qiang, Xu, Sheng-Quan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918254/
https://www.ncbi.nlm.nih.gov/pubmed/31717580
http://dx.doi.org/10.3390/plants8110485
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author Somaratne, Yamuna
Guan, De-Long
Abbood, Nibras Najm
Zhao, Liang
Wang, Wen-Qiang
Xu, Sheng-Quan
author_facet Somaratne, Yamuna
Guan, De-Long
Abbood, Nibras Najm
Zhao, Liang
Wang, Wen-Qiang
Xu, Sheng-Quan
author_sort Somaratne, Yamuna
collection PubMed
description Eragrostis of the tribe Eragrostideae is a taxonomically complex genus, because of its polyploid nature and the presence of similar morphological characters among its species. However, the relationship between these morphologically indistinguishable species at the genomic level has not yet been investigated. Here, we report the complete chloroplast genome of E. pilosa and compare its genome structures, gene contents, simple sequence repeats (SSRs), sequence divergence, codon usage bias, and Kimura 2-parameter (K2P) interspecific genetic distances with those of other Eragrostideae species. The E. pilosa chloroplast genome was 134,815 bp in length and contained 132 genes and four regions, including a large single-copy region (80,100 bp), a small single-copy region (12,661 bp), and a pair of inverted repeats (21,027 bp). The average nucleotide diversity between E. pilosa and E. tef was estimated to be 0.011, and 0.01689 among all species. The minimum and maximum K2P interspecific genetic distance values were identified in psaA (0.007) and matK (0.029), respectively. Of 45 SSRs, eight were shared with E. tef, all of which were in the LSC region. Phylogenetic analysis resolved the monophyly of the sampled Eragrostis species and confirmed the close relationship between E. pilosa and E. tef. This study provides useful chlorophyll genomic information for further species identification and phylogenetic reconstruction of Eragrostis species.
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spelling pubmed-69182542019-12-24 Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae) Somaratne, Yamuna Guan, De-Long Abbood, Nibras Najm Zhao, Liang Wang, Wen-Qiang Xu, Sheng-Quan Plants (Basel) Article Eragrostis of the tribe Eragrostideae is a taxonomically complex genus, because of its polyploid nature and the presence of similar morphological characters among its species. However, the relationship between these morphologically indistinguishable species at the genomic level has not yet been investigated. Here, we report the complete chloroplast genome of E. pilosa and compare its genome structures, gene contents, simple sequence repeats (SSRs), sequence divergence, codon usage bias, and Kimura 2-parameter (K2P) interspecific genetic distances with those of other Eragrostideae species. The E. pilosa chloroplast genome was 134,815 bp in length and contained 132 genes and four regions, including a large single-copy region (80,100 bp), a small single-copy region (12,661 bp), and a pair of inverted repeats (21,027 bp). The average nucleotide diversity between E. pilosa and E. tef was estimated to be 0.011, and 0.01689 among all species. The minimum and maximum K2P interspecific genetic distance values were identified in psaA (0.007) and matK (0.029), respectively. Of 45 SSRs, eight were shared with E. tef, all of which were in the LSC region. Phylogenetic analysis resolved the monophyly of the sampled Eragrostis species and confirmed the close relationship between E. pilosa and E. tef. This study provides useful chlorophyll genomic information for further species identification and phylogenetic reconstruction of Eragrostis species. MDPI 2019-11-09 /pmc/articles/PMC6918254/ /pubmed/31717580 http://dx.doi.org/10.3390/plants8110485 Text en © 2019 by the authors. 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 (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Somaratne, Yamuna
Guan, De-Long
Abbood, Nibras Najm
Zhao, Liang
Wang, Wen-Qiang
Xu, Sheng-Quan
Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title_full Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title_fullStr Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title_full_unstemmed Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title_short Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
title_sort comparison of the complete eragrostis pilosa chloroplast genome with its relatives in eragrostideae (chloridoideae; poaceae)
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6918254/
https://www.ncbi.nlm.nih.gov/pubmed/31717580
http://dx.doi.org/10.3390/plants8110485
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