Abstract
The Millettioid/Phaseoloid (MP) clade from the subfamily Papilionoideae (Leguminosae) consists of six tribes and ca. 3,000 species. Previous studies have revealed some plastome structural variations (PSVs) within this clade. However, many deep evolutionary relationships within the clade remain unresolved. Due to limited taxon sampling and few genetic markers in previous studies, our understanding of the evolutionary history of this clade is limited. To address this issue, we sampled 43 plastomes (35 newly sequenced) representing all the six tribes of the MP clade to examine genomic structural variations and phylogenetic relationships. Plastomes of the species from the MP clade were typically quadripartite (size ranged from 140,029 to 160,040 bp) and contained 109–111 unique genes. We revealed four independent gene losses (ndhF, psbI, rps16, and trnS-GCU), multiple IR-SC boundary shifts, and six inversions in the tribes Desmodieae, Millettieae, and Phaseoleae. Plastomes of the species from the MP clade have experienced significant variations which provide valuable information on the evolution of the clade. Plastid phylogenomic analyses using Maximum Likelihood and Bayesian methods yielded a well-resolved phylogeny at the tribal and generic levels within the MP clade. This result indicates that plastome data is useful and reliable data for resolving the evolutionary relationships of the MP clade. This study provides new insights into the phylogenetic relationships and PSVs within this clade.
Highlights
The plastid genome usually shows a quadripartite structure including a large-single-copy (LSC, 60–90 kb) region, a small-single-copy (SSC, 7–27 kb) region, and a pair of inverted repeats (IR, 20–76 kb) (Raubeson and Jansen, 2005; Zhang et al, 2018)
The IR ranged from 24,111 bp in Desmodium renifolium Schindl. of Desmodieae to 30,644 bp in C. cathartica (Supplementary Table S2)
Gene Loss and Pseudogenization Events Previous studies documented the loss of the genes rpl22 and infA in Lotus japonicus (Regel) K.Larsen of the Robinioid clade (Kato et al, 2000), Trifolium subterraneum L. of the IRLC (Cai et al, 2008), and G. max of the MP clade (Saski et al, 2005); this study confirmed the loss of both genes in all studied species of this clade
Summary
The plastid genome (plastome) usually shows a quadripartite structure including a large-single-copy (LSC, 60–90 kb) region, a small-single-copy (SSC, 7–27 kb) region, and a pair of inverted repeats (IR, 20–76 kb) (Raubeson and Jansen, 2005; Zhang et al, 2018). Some species of Leguminosae, especially those of the subfamily Papilionoideae, have acquired significant plastome structural variations (PSVs) during their evolution. These PSVs includes loss of IR (e.g., Lavin et al, 1990; Doyle et al, 1996), gene or plastome segment inversion (Choi and Choi, 2017), IR expansion, and/or contraction (Choi and Choi, 2017), and gene loss (Jansen et al, 2007; Sabir et al, 2014; Asaf et al, 2017). Only a few studies have examined PSV in the Millettioid/Phaseoloid clade (hereafter referred as the MP clade), one of the most species-rich clades within subfamily Papilionoideae
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