Departmental Papers (Dental)
Complete Plastid Genome Sequence of the Chickpea (Cicer Arietinum) and the Phylogenetic Distribution of rps12 and clpP Intron Losses Among Legumes (Leguminosae)
Date of this Version
Molecular Phylogenetics and Evolution
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.
© <2008>. This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/
Plastid genetic engineering, Genome evolution, Phylogeny of legumes, Leguminosae, Intron loss, Chickpea, Cicer
Jansen, R. K., Wojciechowski, M. F., Sanniyasi, E., Lee, S., & Daniell, H. (2008). Complete Plastid Genome Sequence of the Chickpea (Cicer Arietinum) and the Phylogenetic Distribution of rps12 and clpP Intron Losses Among Legumes (Leguminosae). Molecular Phylogenetics and Evolution, 48 (3), 1204-1217. http://dx.doi.org/10.1016/j.ympev.2008.06.013
Date Posted: 01 March 2022
This document has been peer reviewed.
At the time of publication, author Henry Daniell was affiliated with the University of Central Florida. Currently, he is a faculty member at the School of Dental Medicine at the University of Pennsylvania.