Evolutionary and biotechnology implications of plastid genome variation in the inverted‐repeat‐lacking clade of legumes

Abstract

SummaryLand plant plastid genomes (plastomes) provide a tractable model for evolutionary study in that they are relatively compact and gene dense. Among the groups that display an appropriate level of variation for structural features, the inverted-repeat-lacking clade (IRLC) of papilionoid legumes presents the potential to advance general understanding of the mechanisms of genomic evolution. Here, are presented six complete plastome sequences from economically important species of the IRLC, a lineage previously represented by only five completed plastomes. A number of characters are compared across the IRLC including gene retention and divergence, synteny, repeat structure and functional gene transfer to the nucleus. The loss of clpP intron 2 was identified in one newly sequenced member of IRLC, Glycyrrhiza glabra. Using deeply sequenced nuclear transcriptomes from two species helped clarify the nature of the functional transfer of accD to the nucleus in Trifolium, which likely occurred in the lineage leading to subgenus Trifolium. Legumes are second only to cereal crops in agricultural importance based on area harvested and total production. Genetic improvement via plastid transformation of IRLC crop species is an appealing proposition. Comparative analyses of intergenic spacer regions emphasize the need for complete genome sequences for developing transformation vectors for plastid genetic engineering of legume crops.

The distinct plastid genome structure of Maackia fauriei (Fabaceae: Papilionoideae) and its systematic implications for genistoids and tribe Sophoreae

“…Recent progress in the sequencing of legume plastomes has provided a great deal of valuable data [30, 32, 45, 55–59] that can be used to make phylogenetic inferences based on a “plastome-scale data set” [29]. Those approaches have become more common since the development of next-generation DNA sequencing [28, 30, 60].…”

Enhancing faba bean (Vicia faba L.) genome resources

“…However, the faba bean mitochondrial genome, which was annotated using plasmid/fosmid libraries, shows extensive repetitive content and a low degree of homology to other sequenced mitochondrial genomes (Negruck, 2013). A study on the inverted-repeat-lacking clade of legumes showed that L. culinaris and V. faba have plastomes that are smaller in size than other chloroplast genomes, but they have similar levels (6.7%) of repetitive DNA (Sabir et al , 2014). However, a blastn analysis of all intergenic spacer (IGS) regions from the sequenced plastomes failed to produce any hits for the V. faba sequence in the nucleotide database in GenBank (Sabir et al , 2014).…”

“…A study on the inverted-repeat-lacking clade of legumes showed that L. culinaris and V. faba have plastomes that are smaller in size than other chloroplast genomes, but they have similar levels (6.7%) of repetitive DNA (Sabir et al , 2014). However, a blastn analysis of all intergenic spacer (IGS) regions from the sequenced plastomes failed to produce any hits for the V. faba sequence in the nucleotide database in GenBank (Sabir et al , 2014). In the following analysis, genomic and transcriptome sequencing were performed on faba bean, providing essential underpinning foundation data that can be used to improve gene identification, which is a prerequisite for future studies on the improvement of key traits of agronomic importance.…”

Chloroplast Genome Sequence of Pigeonpea (Cajanus cajan (L.) Millspaugh) and Cajanus scarabaeoides (L.) Thouars: Genome Organization and Comparison with Other Legumes

“…The monophyly of IR- lacking clade (IRLC) (Wojciechowski et al, 2000) has been confirmed with the help of phylogenetic analysis by using plastid genes matK (Wojciechowski et al, 2004), rbcl (Doyle et al, 1997), trnL intron (Pennington et al, 2001), and ITS regions of nuclear ribosomal DNA (Hu et al, 2002). The chloroplast genomes sequenced from IRLC includes: Trifolium aureum; T. repens; T. grandiflorum and T. subterraneum (clover); C. arietinum (chickpea); M. truncatula (barrel medic); Pisum sativum (pea); Lathyrus sativus (grass pea); Lens culinaris (lentil); Glycyrrhiza glabra (licorice); and Vicia faba (broad bean) (Saski et al, 2005; Cai et al, 2008; Jansen et al, 2008; Magee et al, 2010; Sabir et al, 2014). Also it is now believed that loss of IR made the chloroplast genome more prone to rearrangements, like a 50 kb inversion reported in mung bean (Palmer and Thompson, 1982), is present in most members of the papilionoideae subfamily which changes the gene order between trnK and accD genes in the LSC region (Palmer et al, 1988).…”