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Keywords = Eragrostideae

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18 pages, 52587 KB  
Article
Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae)
by Kuan Liu, Rong Wang, Xiu-Xiu Guo, Xue-Jie Zhang, Xiao-Jian Qu and Shou-Jin Fan
Plants 2021, 10(1), 109; https://doi.org/10.3390/plants10010109 - 6 Jan 2021
Cited by 25 | Viewed by 4010
Abstract
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome [...] Read more.
Eragrostideae Stapf, the second-largest tribe in Chloridoideae (Poaceae), is a taxonomically complex tribe. In this study, chloroplast genomes of 13 Eragrostideae species were newly sequenced and used to resolve the phylogenetic relationships within Eragrostideae. Including seven reported chloroplast genomes from Eragrostideae, the genome structure, number and type of genes, codon usage, and repeat sequences of 20 Eragrostideae species were analyzed. The length of these chloroplast genomes varied from 130,773 bp to 135,322 bp. These chloroplast genomes showed a typical quadripartite structure, including a large single-copy region (77,993–80,643 bp), a small single-copy region (12,410–12,668 bp), and a pair of inverted repeats region (19,394–21,074 bp). There were, in total, 129–133 genes annotated in the genome, including 83–87 protein-coding genes, eight rRNA genes, and 38 tRNA genes. Forward and palindromic repeats were the most common repeat types. In total, 10 hypervariable regions (rpl22, rpoA, ndhF, matK, trnGUCC-trnTGGU, ndhFrpl32, ycf4cemA, rpl32trnLUAG, trnGGCCtrnfMCAU, and ccsAndhD) were found, which can be used as candidate molecular markers for Eragrostideae. Phylogenomic studies concluded that Enneapogon diverged first, and Eragrostis including Harpachne is the sister to Uniola. Furthermore, Harpachne harpachnoides is considered as a species of Eragrostis based on morphological and molecular evidence. In addition, the interspecies relationships within Eragrostis are resolved based on complete chloroplast genomes. This study provides useful chloroplast genomic information for further phylogenetic analysis of Eragrostideae. Full article
(This article belongs to the Special Issue Plant Evolution, Systematics, and Chloroplast Genome)
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14 pages, 4165 KB  
Article
Comparison of the Complete Eragrostis pilosa Chloroplast Genome with Its Relatives in Eragrostideae (Chloridoideae; Poaceae)
by Yamuna Somaratne, De-Long Guan, Nibras Najm Abbood, Liang Zhao, Wen-Qiang Wang and Sheng-Quan Xu
Plants 2019, 8(11), 485; https://doi.org/10.3390/plants8110485 - 9 Nov 2019
Cited by 15 | Viewed by 3869
Abstract
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, [...] Read more.
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. Full article
(This article belongs to the Special Issue Plant Bioinformatics)
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