Development of genomic resources for the genus Celtis (Cannabaceae) based on genome skimming data

Celtis is a Cannabaceae genus of 60e70 species of trees,or rarely shrubs,commonly known as hackberries.This woody genus consists of very valuable forest plants that provide important wildlife habitat for birds and mammals.Although previous studies have identified its phylogenetic position,interspecific relationships within Celtis remain unclear.In this study,we generated genome skimming data from five Celtis species to analyze phylogenetic relationships within the genus and develop genome resources.The plastomes of Celtis ranged in length from 158,989 bp to 159,082 bp,with a typical angiosperm quadripartite structure,and encoded a total of 132 genes with 20 duplicated in the IRs.Comparative analyses showed that plastome content and structure were relatively conserved.Whole plastomes showed no signs of gene loss,translocations,inversions,or genome rearrangement.Six plastid hotspot regions(trnH-psbA,psbA-trnK,trnG-trnR,psbC-trnS,cemA-petA and rps8-rpl14),4097 polymorphic nuclear SSRs,as well as 62 low or single-copy gene fragments were identified within Celtis.Moreover,the phylogenetic relationships based on the complete plastome sequences strongly endorse the placement of C.biondii as sister to the((((C.koraiensis,C.sinensis),C.tetrandra),C.julianae),C.cerasifera)clade.These findings and the genetic resources developed here will be conducive to further studies on the genus Celtis involving phylogeny,population genetics,and conservation biology.

Genetic diversity and structure of the endemic and endangered species Aristolochia delavayi growing along the Jinsha River

The traditional medicinal plant,and endangered species Aristolochia delavayi(Aristolochiaceae)is an endemic species in China and occurs in the warm and dry areas along the Jinsha river.It is also a specific host of the larvae of Byasa daemonius,a vulnerable butterfly.In this study,15 pairs of polymorphic microsatellite primers of A.delavayi were designed and screened based on the Simple Sequence Repeats(SSR)loci found by using the results of genome skimming.Based on these 15 SSR markers,the genetic diversity and structure of 193 individuals from ten natural populations were analyzed in detail.In comparison to other endemic and endangered plants in the region,the population of A.delavayi possess a relatively high genetic diversity(He=0.550,I=1.112).AMOVA analysis showed that 68.4%of the total genetic diversity was within populations and 31.6%of the variation occurred among populations.There was a significant genetic differentiation among natural populations of A.delavayi detectable,with low gene flow(Nm=0.591).This might be attributed to geographical barriers and limited seed dispersal.To test the isolation by distance(IBD),we performed Mantel test,which showed a significant correlation between the geographic and genetic distances.In order to cope with the possible biases caused by IBD,we additionally performed Bayesian genetic cluster analyses and principal coordinate analysis(PCoA).The final cluster analysis revealed three groups with distinct geographical distribution.Habitat fragmentation and limited gene flow between these populations may be the main reasons for the current genetic structure.For conservation of this species,we suggest to divide its populations into three protection management units,with subsequent focus on the Yongsheng and Luquan populations which experienced a genetic bottleneck event in the past.

Phylogenetic estimation and morphological evolution of Alsineae(Caryophyllaceae)shed new insight into the taxonomic status of the genus Pseudocerastium

Pseudocerastium is a monotypic genus in Caryophyllaceae endemic to China.The genus has been widely accepted since it was described in 1998,however its phylogenetic position within Caryophyllaceae has never been studied.In the present study,the whole plastid genome and nuclear ribosomal internal transcribed spacer(ITS)sequences of Pseudocerastium stellarioides was obtained through genome skimming,and the phylogenetic position of the species was studied for the first time.Plastid phylogenomic analysis of Caryophyllaceae revealed that Pseudocerastium is clustered within the tribe Alsineae with strong support.Phylogenetic analyses based on an enlarged taxon sampling of Alsineae using five DNA regions(matK,rbcL,rps16 intron,trnL-F and ITS)revealed that P.stellarioides was nested deeply within Cerastium with strong support.Analyses of morphological character evolution suggest that the ancestral states in Alsineae include three styles and a six-lobed capsule at the apex,while both Cerastium and Pseudocerastium have five styles and ten lobes at the apex of the capsule,further supporting their close relationship.The species Pseudocerastium stellarioides is similar to Cerastium wilsonii in morphology,but differs in having villous indumentum on the lower part of the filaments and compressed globose seeds.Therefore,based on the present molecular and morphological evidence,the generic name Pseudocerastium is reduced here as a new synonym of Cerastium and the species P.stellarioides is transferred to Cerastium as C.jiuhuashanense.

An updated classification for the hyper-diverse genus Corydalis(Papaveraceae: Fumarioideae)based on phylogenomic and morphological evidence

The genus Corydalis, with ca. 530 species, has long been considered taxonomically challenging because of its great variability. Previous molecular analyses,based on a few molecular markers and incomplete taxonomic sampling, were clearly inadequate to delimit sections and subgenera. We have performed phylogenetic analyses of Corydalis and related taxa,using 65 shared protein-coding plastid genes from313 accessions(including 280 samples of ca. 226species of Corydalis) and 152 universal low-copy nuclear genes from 296 accessions(including 271samples of Corydalis) covering all 42 previously recognized sections and five independent “series”.Phylogenetic trees were inferred using Bayesian Inference and Maximum Likelihood. Eight selected morphological characters were estimated using ancestral state reconstructions. Results include:(i) of the three subgenera of Corydalis, two are fully supported by both the plastid and nuclear data;the third,subg. Cremnocapnos, is weakly supported by plastid DNA only, whereas in the nuclear data the two included sections form successive outgroups to the rest of the genus;(ii) among all 42 sections and five“series”, 25 sections and one “series” are resolved as monophyletic in both data sets;(iii) the common ancestor of Corydalis is likely to be a perennial plant with a taproot, yellow flowers with a short saccate spur, linear fruits with recurved fruiting pedicels, and seeds with elaiosomes;(iv) we provide a new classification of Corydalis with four subgenera(of which subg. Bipapillatae is here newly described), 39 sections, 16 of which are consistent with the previous classification, 16 sections have been recircumscribed, one section has been reinstated and six new sections are established. Characters associated with lifespan, underground structures, floral spur, fruit and elaiosomes are important for the recognition of subgenera and sections. These new phylogenetic analyses combined with ancestral character reconstructions uncovered previously unrecognized relationships, and greatly improved our understanding of the evolution of the genus.

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.