A review for the breeding of orchids: Current achievements and prospects

Orchids are horticultural plants with significant ornamental and economic value.Increasing market circulation and rising trade in orchids is forcing breeders to develop varieties with unique characteristics,including flower color,morphology,and resistance using a range of approaches,including traditional and molecular breeding.Advances in high-throughput technologies have generated extensive data sets with greater sequencing depths and broader coverage,providing the potential for discovering new genes/pathways that give rise to key traits.Several attempts have been made to use emerging molecular and omics methods to accelerate the breeding process in certain of the commercially valuable orchids.This review consolidates current approaches and achievements in orchid breeding and discusses their future applications for improving the resistance,ornamental,and other valuable characteristics of these plants.

The genome sequence of star fruit(Averrhoa carambola)

Oxalidaceae is one of the most important plant families in horticulture,and its key commercially relevant genus,Averrhoa,has diverse growth habits and fruit types.Here,we describe the assembly of a high-quality chromosomescale genome sequence for Averrhoa carambola(star fruit).Ks distribution analysis showed that A.carambola underwent a whole-genome triplication event,i.e.,the gamma event shared by most eudicots.Comparisons between A.carambola and other angiosperms also permitted the generation of Oxalidaceae gene annotations.We identified unique gene families and analyzed gene family expansion and contraction.This analysis revealed significant changes in MADS-box gene family content,which might be related to the cauliflory of A.carambola.In addition,we identified and analyzed a total of 204 nucleotide-binding site,leucine-rich repeat receptor(NLR)genes and 58 WRKY genes in the genome,which may be related to the defense response.Our results provide insights into the origin,evolution and diversification of star fruit.

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.

Comparative analysis of plastomes in Oxalidaceae:Phylogenetic relationships and potential molecular markers

The wood sorrel family,Oxalidaceae,is mainly composed of annual or perennial herbs,a few shrubs,and trees distributed from temperate to tropical zones.Members of Oxalidaceae are of high medicinal,ornamental,and economic value.Despite the rich diversity and value of Oxalidaceae,few molecular markers or plastomes are available for phylogenetic analysis of the family.Here,we reported four new whole plastomes of Oxalidaceae and compared them with plastomes of three species in the family,as well as the plastome of Rourea microphylla in the closely related family Connaraceae.The eight plastomes ranged in length from 150,673 bp(Biophytum sensitivum)to 156,609 bp(R.microphylla).Genome annotations revealed a total of 129e131 genes,including 83e84 protein-coding genes,eight rRNA genes,37 tRNA genes,and two to three pseudogenes.Comparative analyses showed that the plastomes of these species have minor variations at the gene level.The smaller plastomes of herbs B.sensitivum and three Oxalis species are associated with variations in IR region sizes,intergenic region variation,and gene or intron loss.We identified sequences with high variation that may serve as molecular markers in taxonomic studies of Oxalidaceae.The phylogenetic trees of selected superrosid representatives based on 76 protein-coding genes corroborated the Oxalidaceae position in Oxalidales and supported it as a sister to Connaraceae.Our research also supported the monophyly of the COM(Celastrales,Oxalidales,and Malpighiales)clade.

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.