Comparative and Phylogenetic Analysis of Complete Chloroplast Genomes in Eragrostideae (Chloridoideae, Poaceae).
Eragrostideae
Eragrostis
chloroplast genome
comparative genomics
phylogenomics
Journal
Plants (Basel, Switzerland)
ISSN: 2223-7747
Titre abrégé: Plants (Basel)
Pays: Switzerland
ID NLM: 101596181
Informations de publication
Date de publication:
06 Jan 2021
06 Jan 2021
Historique:
received:
03
12
2020
revised:
03
01
2021
accepted:
04
01
2021
entrez:
9
1
2021
pubmed:
10
1
2021
medline:
10
1
2021
Statut:
epublish
Résumé
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 (
Identifiants
pubmed: 33419221
pii: plants10010109
doi: 10.3390/plants10010109
pmc: PMC7825611
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : National Natural Science Foundation of China
ID : 31470298
Références
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W273-9
pubmed: 15215394
Ann Bot. 2011 Feb;107(2):321-5
pubmed: 21098824
J Mol Evol. 2009 Oct;69(4):311-8
pubmed: 19777151
Methods Enzymol. 2005;395:348-84
pubmed: 15865976
Sci Rep. 2017 May 8;7(1):1555
pubmed: 28484234
Bioinformatics. 2012 Jun 15;28(12):1647-9
pubmed: 22543367
Curr Genet. 1996 May;29(6):572-81
pubmed: 8662197
Plant J. 2005 Oct;44(2):237-44
pubmed: 16212603
PLoS One. 2012;7(5):e36869
pubmed: 22606302
BMC Evol Biol. 2006 Oct 04;6:77
pubmed: 17020608
Mol Biol Evol. 2013 Apr;30(4):772-80
pubmed: 23329690
Mol Biol Evol. 2003 Jun;20(6):988-93
pubmed: 12716982
Plant Methods. 2019 May 21;15:50
pubmed: 31139240
Bioinformatics. 2017 Aug 15;33(16):2583-2585
pubmed: 28398459
Science. 2013 Feb 1;339(6119):571-4
pubmed: 23372012
Bioinformatics. 2018 Sep 1;34(17):3030-3031
pubmed: 29659705
Am J Bot. 2010 May;97(5):874-92
pubmed: 21622452
Bioinformatics. 2014 May 1;30(9):1312-3
pubmed: 24451623
Mitochondrial DNA B Resour. 2019 Nov 22;4(2):4216-4217
pubmed: 33366389
Plants (Basel). 2019 Nov 09;8(11):
pubmed: 31717580
Genome Biol Evol. 2019 Oct 1;11(10):2789-2796
pubmed: 31504501
Mol Phylogenet Evol. 2016 Dec;105:1-14
pubmed: 27554759
Genetics. 1999 Oct;153(2):943-7
pubmed: 10511569
PeerJ. 2017 Sep 18;5:e3820
pubmed: 28948105
Plant J. 2000 Apr;22(2):97-104
pubmed: 10792825
Curr Biol. 2002 Jan 22;12(2):R62-4
pubmed: 11818081
Front Plant Sci. 2016 Jun 14;7:843
pubmed: 27379132
Sci Rep. 2017 Sep 14;7(1):11649
pubmed: 28912544
Curr Genet. 1993 Feb;23(2):160-5
pubmed: 8431958
Mol Phylogenet Evol. 2010 May;55(2):580-98
pubmed: 20096795
Gene. 1990 Mar 1;87(1):23-9
pubmed: 2110097
Mitochondrial DNA B Resour. 2020 Jan 7;5(1):396-397
pubmed: 33366573
Nucleic Acids Res. 2019 Jul 2;47(W1):W59-W64
pubmed: 30949694
Trends Ecol Evol. 2001 Mar 1;16(3):142-147
pubmed: 11179578
Plants (Basel). 2020 Jan 02;9(1):
pubmed: 31906501
Am J Bot. 2007 Mar;94(3):275-88
pubmed: 21636401
J Mol Evol. 2003 May;56(5):616-29
pubmed: 12698298
Nucleic Acids Res. 2001 Nov 15;29(22):4633-42
pubmed: 11713313
PLoS One. 2013 Oct 18;8(10):e78568
pubmed: 24205264
Front Plant Sci. 2017 Mar 07;8:304
pubmed: 28326093
Am J Bot. 2003 Jan;90(1):116-22
pubmed: 21659086