Nuclear phylogeny and insights into wholegenome duplications and reproductive development of Solanaceae plants

Solanaceae,the nightshade family,have2700 species,including the important crops potato and tomato,ornamentals,and medicinal plants.Several sequenced Solanaceae genomes show evidence for wholegenome duplication(WGD),providing an excellent opportunity to investigate WGD and its impacts.Here,we generated 93 transcriptomes/genomes and combined them with 87 public datasets,for a total of 180 Solanaceae species representing all four subfamilies and 14 of 15 tribes.Nearly 1700 nuclear genes from these transcriptomic/genomic datasets were used to reconstruct a highly resolved Solanaceae phylogenetic tree with six major clades.The Solanaceae tree supports four previously recognized subfamilies(Goetzeioideae,Cestroideae,Nicotianoideae,and Solanoideae)and the designation of three other subfamilies(Schizanthoideae,Schwenckioideae,and Petunioideae),with the placement of several previously unassigned genera.We placed a Solanaceae-specific whole-genome triplication(WGT1)at81 million years ago(mya),before the divergence of Schizanthoideae from other Solanaceae subfamilies at73 mya.In addition,we detected two gene duplication bursts(GDBs)supporting proposed WGD events and four other GDBs.An investigation of the evolutionary histories of homologs of carpel and fruit developmental genes in 14 gene(sub)families revealed that 21 gene clades have retained gene duplicates.These were likely generated by the Solanaceae WGT1 and may have promoted fleshy fruit development.This study presents a well-resolved Solanaceae phylogeny and a new perspective on retained gene duplicates and carpel/fruit development,providing an improved understanding of Solanaceae evolution.

Phylotranscriptomic insights into Asteraceae diversity,polyploidy,and morphological innovation

Biodiversity is not evenly distributed among relatedgroups,raising questions about the factors con-tributing to such disparities.The sunflower family(Asteraceae,>26,000 species)is among the largestand most diverse plant families,but its species di-versity is concentrated in a few subfamilies,pro-viding an opportunity to study the factors affectingbiodiversity.Phylotranscriptomic analyses here of244 transcriptomes and genomes produced a phy-logeny with strong support for the monophyly ofAsteraceae and the monophyly of most subfamiliesand tribes.This phylogeny provides a reference fordetecting changes in diversification rates and pos-sible factors affecting Asteraceae diversity,whichinclude global climate shifts,whole‐genome dupli-cations(WGDs),and morphological evolution.Theorigin of Asteraceae was estimated at~83 Mya,with most subfamilies having diverged before theCretaceous–Paleocene boundary.Phylotran-scriptomic analyses supported the existence of 41WGDs in Asteraceae.Changes to herbaceousnessand capitulescence with multipleflower‐like capitula,often with distinctflorets and scaly pappus/re-ceptacular bracts,are associated with multiple up-shifts in diversification rate.WGDs might have con-tributed to the survival of early Asteraceae byproviding new genetic materials to support mor-phological transitions.The resulting competitive ad-vantage for adapting to different niches would haveincreased biodiversity in Asteraceae.