TY - JOUR
T1 - Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)
AU - Jansen, Robert K.
AU - Wojciechowski, Martin
AU - Sanniyasi, Elumalai
AU - Lee, Seung Bum
AU - Daniell, Henry
N1 - Funding Information:
Investigations reported in this article were supported in part by Grants from USDA 3611-21000-017-00D and NIH R01 GM 63879 to H.D. Research by R.K.J. was supported, in part, by NSF ATOL Grant DEB0120709. M.F.W. was supported, in part, by NSF Grant DEB0542958. The authors thank Matt Lavin, Alfonso Delgado-Salinas, Jennifer Trusty, Kelly Steele, Jer-Ming Hu, R. Toby Pennington, Mats Thulin, Aaron Listen, herbaria of The Royal Botanic Gardens at Kew (K), Edinburgh (E), Munich (M/MSB), and the Arizona State University Vascular Plant Herbarium (ASU) for tissue or DNA samples, and Dr. Michael Bausher (USDA) for help in early stages of genome sequencing. We also thank Anne Bruneau and an anonymous reviewer for their helpful comments on the manuscript.
PY - 2008/9
Y1 - 2008/9
N2 - Chickpea (Cicer arietinum, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes rps16, infA, and ycf4 are absent in the chickpea plastid genome, and ndhB has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The clpP intron has been lost exclusively in taxa from the temperate "IR-lacking clade" (IRLC), whereas the rps12 intron has been lost in most members of the IRLC (with the exception of Wisteria, Callerya, Afgekia, and certain species of Millettia, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the rps12 intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.
AB - Chickpea (Cicer arietinum, Leguminosae), an important grain legume, is widely used for food and fodder throughout the world. We sequenced the complete plastid genome of chickpea, which is 125,319 bp in size, and contains only one copy of the inverted repeat (IR). The genome encodes 108 genes, including 4 rRNAs, 29 tRNAs, and 75 proteins. The genes rps16, infA, and ycf4 are absent in the chickpea plastid genome, and ndhB has an internal stop codon in the 5′exon, similar to other legumes. Two genes have lost their introns, one in the 3′exon of the transpliced gene rps12, and the one between exons 1 and 2 of clpP; this represents the first documented case of the loss of introns from both of these genes in the same plastid genome. An extensive phylogenetic survey of these intron losses was performed on 302 taxa across legumes and the related family Polygalaceae. The clpP intron has been lost exclusively in taxa from the temperate "IR-lacking clade" (IRLC), whereas the rps12 intron has been lost in most members of the IRLC (with the exception of Wisteria, Callerya, Afgekia, and certain species of Millettia, which represent the earliest diverging lineages of this clade), and in the tribe Desmodieae, which is closely related to the tribes Phaseoleae and Psoraleeae. Data provided here suggest that the loss of the rps12 intron occurred after the loss of the IR. The two new genomic changes identified in the present study provide additional support of the monophyly of the IR-loss clade, and resolution of the pattern of the earliest-branching lineages in this clade. The availability of the complete chickpea plastid genome sequence also provides valuable information on intergenic spacer regions among legumes and endogenous regulatory sequences for plastid genetic engineering.
KW - Chickpea
KW - Cicer
KW - Genome evolution
KW - Intron loss
KW - Leguminosae
KW - Phylogeny of legumes
KW - Plastid genetic engineering
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U2 - 10.1016/j.ympev.2008.06.013
DO - 10.1016/j.ympev.2008.06.013
M3 - Article
C2 - 18638561
AN - SCOPUS:50549100831
SN - 1055-7903
VL - 48
SP - 1204
EP - 1217
JO - Molecular Phylogenetics and Evolution
JF - Molecular Phylogenetics and Evolution
IS - 3
ER -