Characterization of the complete chloroplast genome sequence of the IRLC species and its phylogenetic implications

Fabaceae (legumes) are the third largest family of angiosperms which have shown the most structural variation.Currently accepted classification of the legumes based on plastid gene matK includes six subfamilies: Caesalpinioideae, Cercidoideae, Detarioideae, Dialioideae, Duparquetioideae, and Papilionoideae. Gene order and gene content in plastomes of all subfamilies except Papilionoideae are highly conserved and similar to the ancestral angiosperm genome organization. Papilionoideae exhibit numerous rearrangements and gene/intron losses and have smaller genome. The remarkable loss of the one of the plastid inverted repeats in the inverted repeat lacking clade (IRLC), a largest legume lineage, is an example of genome variation in papilionoids. This clade comprises ۵۲ genera (e.g., Wisteria, Glycyrrhiza, Astragalus, Colutea, Trifolium, Lathyrus, ...) and ca ۴۰۰۰ species divided into eight tribes. Furthermore, plastome in IRLC show other rearrangements of gene order and gene content. For example, ycf۴ in some species of Lathyrus and Pisum (both from the tribe Fabeae) is either absent or a pseudogene. Comparative analysis of the chloroplast genomes across the IRLC revealed that ycf۱ gene, which is located in the IR region, is more variable than matK in many taxa and thus suitable for molecular systematics at low taxonomic levels. Furthermore, the monophyly of the IRLC and all its tribes is in accordance with all previous studies.