Complete plastid genome sequence of the chickpea (Cicer arietinum) and the phylogenetic distribution of rps12 and clpP intron losses among legumes (Leguminosae)

Abstract

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.

Different status of the gene for ribosomal protein S16 in the chloroplast genome during evolution of the genus Arabidopsis and closely related species

“…Six complete legume chloroplast genomes have been reported to date (G. max, L. japonicus. M. truncatula, P. vulgaris, C. arietinum, and V. radiata) (Jansen et al, 2008;Tangphatsornruang et al, 2010). A similar tendency to lose the cp rps16 in selfcompatible plants is observed in these species.…”

“…Although the number of genes and their order are generally conserved among angiosperm chloroplast genomes, exceptional gene losses have been identified (e.g., rpl33 in Phaseolus vulgaris (Guo et al, 2007) and Vigna radiata (Tangphatsornruang et al, 2010), infA in almost all rosid species (Millen et al, 2001), rpl32 in the Populus genus (Okumura et al, 2006;Steane, 2005), rps16 in Medicago truncatula (Saski et al, 2005), P. vulgaris (Guo et al, 2007), Cicer arietinum (Jansen et al, 2008), V. radiata (Tangphatsornruang et al, 2010), and the Populus genus (Okumura et al, 2006;Steane, 2005)). It is also possible that genes that have been transferred or substituted recently in evolution remain in the chloroplast genome as remnants when gene transfer or substitution has occurred.…”

Piecing together the puzzle of parasitic plant plastome evolution

“…In tobacco, for example, 20 group II introns have to be spliced to enable the generation of translatable transcripts. Individual intron losses, for example, for the clpP, rpl2, rps12 and atpF genes have been recorded in a few angiosperm lineages (Schmitz-Linneweber et al 2001;Jansen et al 2008), but can generally be considered an exception. Therefore, it came as a surprise when the sequence analysis of the plastomes of C. gronovii (Funk et al 2007) and later also C. obtusiflora (McNeal et al , 2009) revealed the most extensive intron losses ever detected in any species: In both cases, all but one group IIa intron-intron 2 of clpP-were lost.…”

Lentil

“…25 kb). The clade includes all the members of the tribes Cicereae, Hedysareae, Trifolieae, and Vicieae, as well as at least three other genera (Wojciechowski 2006 ;Jansen et al 2008 ). Thus, the interesting crop legume genera such as Trifolium, Medicago , and Cicer all hold a close phylogenetic relation to lentil and other Vicieae species.…”