Phylogenomics and biogeography of Wisteria (Fabaceae), with implication on plastome evolution of inverted repeat-lacking clade

Abstract

Background: The inverted repeat-lacking clade (IRLC) of Fabaceae is characterized by loss of an IR region in plastomes. Both the loss of an IR region and the life history may have affected the evolution of the plastomes in the clade. Nevertheless, few studies have been done to test the impact explicitly. Wisteria , an important member of IRLC and has a disjunct distribution between eastern Asia and eastern North America, has confused interspecific relationships and biogeography, which need to elucidate in depth. Results: The plastome of six newly sequenced Wisteria species and a Millettia japonica ranged from 130,116 to 132,547 bp. Phylogenetic analyses recognized two major clades in IRLC: Glycyrrhiza - Millettia - Wisteria clade and a clade containing the remaining genera. North American Wisteria species and Asian species formed reciprocal clades. Within Asian clade, each of the two Japanese species was sister to a species in the Asian continent. A ~16kb inversion from ndh F to ycf 1 in all IRLC species. Wisteria and Millettia japonica have two intron of rps 12 gene but all other IRLC species just have one. Synonymous substitution rates ( d S ) of protein coding genes were higher in the IRLC species than non-IRLC species. Woody species have lower substitutions rates than herbs. Wisteria may have originated in East Asia by the boundary of Oligocene and Miocene and the eastern Asian-eastern North American disjunction formed in the Late Miocene, while two vicariance events formed the disjunct distributions between the Asian continent and the Japanese islands in the Quaternary. Conclusions: In the IRLC clade, Wisteria , Milletia japonica and Glycyrrhiza form a clade to the remaining genera, most of which are herbaceous. Both the loss of one IR region and the herbaceous habit elevated mutation rates of the plastomes. Multiple vicariance events between eastern Asia and eastern North America, and between the Asian continent and the Japanese Islands may have promoted speciation of Wisteria since the Late Miocene. Plastomes contain rich genetic diversity for studying genetic structure and migration of populations in response to climatic changes, which benefits conservation of rare and endangered species.