A chromosome-scale reference genome of Aquilegia oxysepala var.kansuensis

The genus Aquilegia(Ranunculaceae)has been cultivated as ornamental and medicinal plants for centuries.With petal spurs of strikingly diverse size and shape,Aquilegia has also been recognized as an excellent system for evolutionary studies.Pollinator‐mediated selection for longer spurs is believed to have shaped the evolution of this genus,especially the North American taxa.Recently,however,an opposite evolutionary trend was reported in an Asian lineage,where multiple origins of mini-or even nonspurred morphs have occurred.Interesting as it is,the lack of genomic resources has limited our ability to decipher the molecular and evolutionary mechanisms underlying spur reduction in this special lineage.Using long-read sequencing(PacBio Sequel),in combination with optical maps(BioNano DLS)and Hi–C,we assembled a high-quality reference genome of A.oxysepala var.kansuensis,a sister species to the nonspurred taxon.The final assembly is approximately 293.2 Mb,94.6%(277.4 Mb)of which has been anchored to 7 pseudochromosomes.A total of 25,571 protein-coding genes were predicted,with 97.2%being functionally annotated.When comparing this genome with that of A.coerulea,we detected a large rearrangement between Chr1 and Chr4,which might have caused the Chr4 of A.oxysepala var.kansuensis to partly deviate from the“decaying”path that was taken before the split of Aquilegia and Semiaquilegia.This high-quality reference genome is fundamental to further investigations on the development and evolution of petal spurs and provides a strong foundation for the breeding of new horticultural Aquilegia cultivars.

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.

A chromosome-scale genome assembly of Artemisia argyi reveals unbiased subgenome evolution and key contributions of gene duplication to volatile terpenoid diversity

Artemisia argyi Le´vl.et Vant.,a perennial Artemisia herb with an intense fragrance,is widely used in traditional medicine in China and many other Asian countries.Here,we present a chromosome-scale genome assembly of A.argyi comprising 3.89 Gb assembled into 17 pseudochromosomes.Phylogenetic and comparative genomic analyses revealed that A.argyi underwent a recent lineage-specificwhole-genomeduplication(WGD)event after divergence fromArtemisia annua,resulting in two subgenomes.Wedeciphered the diploid ancestral genome of A.argyi,and unbiased subgenome evolution was observed.The recent WGD led to a large number of duplicated genes in the A.argyi genome.Expansion of the terpene synthase(TPS)gene family through various types of gene duplication may have greatly contributed to the diversity of volatile terpenoids in A.argyi.In particular,we identified a typical germacrene D synthase gene cluster within the expanded TPS gene family.The entire biosynthetic pathways of germacrenes,(+)-borneol,and(+)-camphor were elucidated in A.argyi.In addition,partial deletion of the amorpha-4,11-diene synthase(ADS)gene and loss of function of ADS homologs may have resulted in the lack of artemisinin production in A.argyi.Our study provides newinsights into the genome evolution of Artemisia and lays a foundation for further improvement of the quality of this important medicinal plant.

Genome resources for the elite bread wheat cultivar Aikang 58 and mining of elite homeologous haplotypes for accelerating wheat improvement

Despite recent progress in crop genomics studies,the genomic changes brought about by modern breeding selection are still poorly understood,thus hampering genomics-assisted breeding,especially in polyploid crops with compound genomes such as common wheat(Triticum aestivum).In this work,we constructed genome resources for the modern elite common wheat variety Aikang 58(AK58).Comparative genomics between AK58 and the landrace cultivar Chinese Spring(CS)shed light on genomic changes that occurred through recent varietal improvement.We also explored subgenome diploidization and divergence in common wheat and developed a homoeologous locus-based genome-wide association study(HGWAS)approach,which was more effective than single homoeolog-based GWAS in unraveling agronomic trait-associated loci.A total of 123 major HGWAs loci were detected using a genetic population derived from AK58 and cs.Elite homoeologous haplotypes(HHs),formed by combinations of subgenomic homoeologs of the associated loci,were found in both parents and progeny,and many could substantially improve wheat yield and related traits.We built a website where users can download genome assembly sequence and annotation data for AK58,perform blast analysis,and run JBrowse.Our work enriches genome resources for wheat,provides new insights into genomic changes during modern wheat improve-.ment,and suggests that efficientmining of elite HHs can make a substantial contribuutionto genomics-assisted breeding in common wheat and other polyploid crops.

WheatCENet:A Database for Comparative Co-expression Network Analysis of Allohexaploid Wheat and Its Progenitors

Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named WheatCENet.WheatCENet is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered therein.Functional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.

Genetic Contribution of Paleopolyploidy to Adaptive Evolution in Angiosperms

Ancient whole-genome duplications (WGDs or polyploidy) are prevalent in plants, and some WGDs occurred during the timing of severe global environmental changes. It has been suggested that WGDs may have contributed to plant adaptation. However, this still lacks empirical evidence at the genetic level to support the hypothesis. Here, we investigated the survivors of gene duplicates from multiple ancient WGD events on the major branches of angiosperm phylogeny, and aimed to explore genetic evidence supporting the significance of polyploidy. Duplicated genes co-retained from three waves of independent WGDs (～120 million years ago [Ma], ～66, and <20 Ma) were investigated in 25 selected species. Gene families functioning in low temperature and darkness were commonly retained gene duplicates after the eight independently occurring WGDs in many lineages around the Cretaceous-Paleocene boundary, when the global cooling and darkness were the two main stresses. Moreover, the commonly retained duplicates could be key factors which may have contributed to the robustness of the critical stress-related pathways. In addition, genome-wide transcription factors (TFs) functioning in stresses tend to retain duplicates after waves of WGDs, and the coselected gene duplicates in many lineages may play critical roles during severe environmental stresses. Collectively, these results shed new light on the significant contribution of paleopolyploidy to plant adaptation during global environmental changes in the evolutionary history of angiosperms.

A Collinearity-Incorporating Homology Inference Strategy for Connecting Emerging Assemblies in the Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

Plant genome sequencing has dramatically increased,and some species even have multiple high-quality reference versions.Demands for clade-specific homology inference and analysis have increased in the pangenomic era.Here we present a novel method,GeneTribe(https://chenym1.github.io/genetribe/),for homology inference among genetically similar genomes that incorporates gene collinearity and shows bet-ter performance than traditional sequence-similarity-based methods in terms of accuracy and scalability.The Triticeae tribe is a typical allopolyploid-rich clade with complex species relationships that includes many important crops,such as wheat,barley,and rye.We built Triticeae-GeneTribe(http://wheat.cau.edu.cn/TGT/),a homology database,by integrating 12 Triticeae genomes and 3 outgroup model genomes and implemented versatile analysis and visualization functions.With macrocollinearity analysis,we were able to construct a refined model illustrating the structural rearrangements of the 4A-5A-7B chromosomes in wheat as two major translocation events.With collinearity analysis at both the macro-and microscale,we illustrated the complex evolutionary history of homologs of the wheat vernalization gene Vm2,which evolved as a combined result of genome translocation,duplication,and polyploidization and gene loss events.Our work provides a useful practice for connecting emerging genome assemblies,with awareness of the extensive polyploidy in plants,and will help researchers efficiently exploit genome sequence re-sources.

Wheat genomic study for genetic improvement of traits in China

Bread wheat(Triticum aestivum L.)is a major crop that feeds 40%of the world’s population.Over the past several decades,advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat,and the genetic basis of agronomically important traits,which promote the breeding of elite varieties.In this review,we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield,end-use traits,flowering regulation,nutrient use efficiency,and biotic and abiotic stress responses,and various breeding strategies that contributed mainly by Chinese scientists.Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools,highthroughput phenotyping platforms,sequencing-based cloning strategies,high-efficiency genetic transformation systems,and speed-breeding facilities.These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process,ultimately contributing to more sustainable agriculture in China and throughout the world.

New insights into the dispersion history and adaptive evolution of taxon Aegilops tauschii in China

Aegilops tauschii,the wild progenitor of wheat D-genome and a valuable germplasm for wheat improvement,has a wide natural distribution from eastern Turkey to China.However,the phylogenetic relationship and dispersion history of Ae.tauschii in China has not been scientifically clarified.In this study,we genotyped 208 accessions(with 104 in China)using dd RAD sequencing and 55K SNP array,and classified the population into six sublineages.Three possible spreading routes or events were identified,resulting in specific distribution patterns,with four sublineages found in Xinjiang,one in Qinghai,two in Shaanxi and one in Henan.We also established the correlation of SNP-based,karyotypebased and spike-morphology-based techniques to demonstrate the internal classification of Ae.tauschii,and developed consensus dataset with 1245 putative accessions by merging data previously published.Our analysis suggested that eight inter-lineage accessions could be assigned to the putative Lineage 3and these accessions would help to conserve the genetic diversity of the species.By developing the consensus phylogenetic relationships of Ae.tauschii,our work validated the hypothesis on the dispersal history of Ae.tauschii in China,and contributed to the efficient and comprehensive germplasm-mining of the species.

A recent burst of gene duplications in Triticeae

Gene duplication provides raw genetic materials for evolution and potentially novel genes for crop improvement.The two seminal genomic studies of Aegilops tauschii both mentioned the large number of genes independently duplicated in recent years,but the duplication mechanism and the evolutionary significance of these gene duplicates have not yet been investigated.Here,we found that a recent burst of gene duplications(hereafter abbreviated as the RBGD)has probably occurred in all sequenced Triticeae species.Further investigations of the characteristics of the gene duplicates and their flanking sequences suggested that transposable element(TE)activity may have been involved in generating the RBGD.We also characterized the duplication timing,retention pattern,diversification,and expression of the duplicates following the evolution of Triticeae.Multiple subgenome-specific comparisons of the duplicated gene pairs clearly supported extensive differential regulation and related functional diversity among such pairs in the three subgenomes of bread wheat.Moreover,several duplicated genes from the RBGD have evolved into key factors that influence important agronomic traits of wheat.Our results provide insights into a unique source of gene duplicates in Triticeae species,which has increased the gene dosage together with the two polyploidization events in the evolutionary history of wheat.

The Genome of Opium Poppy Reveals Evolutionary History of Morphinan Pathway

Plants, as primary producers, have been playing an indispensable role in other organisms’ survival and the balance of whole ecosystem on Earth. Especially, they provide the main source of energy, food, and medicine for human beings, some of which are derived from the primary or secondary metabolites[1].Angiosperms,with more than 300,000 species on Earth,are the largest group of land plants by far.