Initial Characterization of the Chloroplast Genome of Vicia sepium , an Important Wild Resource Plant, and Related Inferences About Its Evolution

Frontiers in Genetics
Chaoyang LiXiaoyun Peng

Abstract

Lack of complete genomic information concerning Vicia sepium (Fabaceae: Fabeae) precludes investigations of evolution and populational diversity of this perennial high-protein forage plant suitable for cultivation in extreme conditions. Here, we present the complete and annotated chloroplast genome of this important wild resource plant. V. sepium chloroplast genome includes 76 protein-coding genes, 29 tRNA genes, 4 rRNA genes, and 1 pseudogene. Its 124,095 bp sequence has a loss of one inverted repeat (IR). The GC content of the whole genome, the protein-coding, intron, tRNA, rRNA, and intergenic spacer regions was 35.0%, 36.7%, 34.6%, 52.3%, 54.2%, and 29.2%, respectively. Comparative analyses with plastids from related genera belonging to Fabeae demonstrated that the greatest variation in the V. sepium genome length occurred in protein-coding regions. In these regions, some genes and introns were lost or gained; for example, ycf4, clpP intron, and rpl16 intron deletions and rpl20 and ORF292 insertions were observed. Twelve highly divergent regions, 66 simple sequence repeats (SSRs) and 27 repeat sequences were also found in these regions. Detailed evolutionary rate analysis of protein-coding genes showed that Vicia species ex...Continue Reading

References

Jan 1, 1987·Journal of Molecular Evolution·H Ochman, A C Wilson
Dec 1, 1987·Proceedings of the National Academy of Sciences of the United States of America·K H WolfeP M Sharp
Jul 8, 1997·Proceedings of the National Academy of Sciences of the United States of America·C W dePamphilisA D Wolfe
Apr 29, 1998·Journal of Molecular Evolution·Z Yang, R Nielsen
Dec 24, 1998·Nucleic Acids Research·G Benson
Nov 20, 2001·Nucleic Acids Research·S KurtzR Giegerich
Jan 22, 2004·Nature Reviews. Genetics·Jeremy N TimmisWilliam Martin
Jun 8, 2004·Bioinformatics·Stacia K WymanJeffrey L Boore
Jun 25, 2004·Nucleic Acids Research·Kelly A FrazerInna Dubchak
Jul 3, 2004·Genome Research·Aaron C E DarlingNicole T Perna
May 4, 2005·Methods in Enzymology·Robert K JansenLiying Cui
May 11, 2005·Trends in Plant Science·William MartinVadim Goremykin
Dec 1, 2007·Proceedings of the National Academy of Sciences of the United States of America·Robert K JansenJeffrey L Boore
Jan 20, 2009·Bioinformatics·Andrew M WaterhouseGeoffrey J Barton
Oct 28, 2010·Genome Research·Alan M MageeKenneth H Wolfe
Dec 15, 2010·Bioinformatics·Marten BoetzerWalter Pirovano
Mar 23, 2011·Plant Molecular Biology·Susann WickeDietmar Quandt
Aug 10, 2011·BMC Genomics·Nabil-Fareed AlikhanScott A Beatson
Jan 19, 2013·Molecular Biology and Evolution·Kazutaka Katoh, Daron M Standley
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jun 11, 2014·Food Chemistry·Elena Pastor-CavadaJavier Vioque
Aug 28, 2015·Applications in Plant Sciences·Daisie I Huang, Quentin C B Cronk
Mar 24, 2016·Molecular Biology and Evolution·Sudhir KumarKoichiro Tamura
Jan 10, 2017·Journal of Animal Physiology and Animal Nutrition·Y F HuangZ X Zhang
Mar 25, 2017·DNA Research : an International Journal for Rapid Publication of Reports on Genes and Genomes·J KellerA Aïnouche
Feb 27, 2018·Frontiers in Plant Science·Yin-Huan WangTing-Shuang Yi

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Datasets Mentioned

BETA
KF042344

Software Mentioned

MEGA7
CpGAVAS
NS
REPuter
ModelTest
SOAPdenovo2
Jalview
MISA Perl Script
SSPACE
DOGMA

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