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.

Nuclear phylotranscriptomics and phylogenomics support numerous polyploidization events and hypotheses for the evolution of rhizobial nitrogenfixing symbiosis in Fabaceae

Fabaceae are the third largest angiosperm family,with 765 genera and~19500 species.They are important both economically and ecologically,and global Fabaceae crops are intensively studied in part for their nitrogen-fixing ability.However,resolution of the intrasubfamilial Fabaceae phylogeny and divergence times has remained elusive,precluding a reconstruction of the evolutionary history of symbiotic nitrogen fixation in Fabaceae.Here,we report a highly resolved phylogeny using>1500 nuclear genes from newly sequenced transcriptomes and genomes of 391 species,along with other datasets,for a total of 463 legumes spanning all 6 subfamilies and 333 of 765 genera.The subfamilies are maximally supported as mono-phyletic.The clade comprising subfamilies Cercidoideae and Detarioideae is sister to the remaining legumes,and Duparquetioideae and Dialioideae are successive sisters to the clade of Papilionoideae and Caesalpinioideae.Molecular clock estimation revealed an early radiation of subfamilies near the K/Pg boundary,marked by mass extinction,and subsequent divergence of most tribe-level clades within~15 million years.Phylogenomic analyses of thousands of gene families support 28 proposed putative whole-genome duplication/whole-genome triplication events across Fabaceae,including those at the ancestors of Fabaceae and five of the subfamilies,and further analyses supported the Fabaceae ancestral polyploidy.The evolution of rhizobial nitrogen-fixing nodulation in Fabaceae was probed by ancestral character reconstruction and phylogenetic analyses of related gene families and the results support the hypotheses of one or two switches)to rhizobial nodulation followed by multiple losses.Collectively,these results provide a foundation for further morphological and functional evolutionary analyses across Fabaceae.

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.

Phylogenomic conflict analyses in the apple genus Malus s.l.reveal widespread hybridization and allopolyploidy driving diversification,with insights into the complex biogeographic history in the Northern Hemisphere

Phylogenomic evidence from an increasing number of studies has demonstrated that different data sets and analytical approaches often reconstruct strongly supported but conflicting relationships.In this study,785 single-copy nuclear genes and 75 complete plastomes were used to infer the phylogenetic relationships and estimate the historical biogeography of the apple genus Malus sensu lato,an economically important lineage disjunctly distributed in the Northern Hemisphere and involved in known and suspected hybridization and allopolyploidy events.The nuclear phylogeny recovered the monophyly of Malus s.l.(including Docynia);however,the genus was supported to be biphyletic in the plastid phylogeny.An ancient chloroplast capture event in the Eocene in western North America best explains the cytonuclear discordance.Our conflict analysis demonstrated that ILS,hybridization,and allopolyploidy could explain the widespread nuclear gene tree discordance.One deep hybridization event(Malus doumeri)and one recent event(Malus coronaria)were detected in Malus s.l.Furthermore,our historical biogeographic analysis integrating living and fossil data supported a widespread East Asianwestern North American origin of Malus s.l.in the Eocene,followed by several extinction and dispersal events in the Northern Hemisphere.We also propose a general workflow for assessing phylogenomic discordance and biogeographic analysis using deep genome skimming data sets.