Lycophyte transcriptomes reveal two whole-genome duplications in Lycopodiaceae:Insights into the polyploidization of Phlegmariurus

Lycophytes are an ancient clade of the non-flowering vascular plants with chromosome numbers that vary from tens to hundreds.They are an excellent study system for examining whole-genome duplications(WGDs),or polyploidization,in spore-dispersed vascular plants.However,a lack of genome sequence data limits the reliable detection of very ancient WGDs,small-scale duplications(SSDs),and recent WGDs.Here,we integrated phylogenomic analysis and the distribution of synonymous substitutions per synonymous sites(Ks)of the transcriptomes of 13 species of lycophytes to identify,locate,and date multiple WGDs in the lycophyte family Lycopodiaceae.Additionally,we examined the genus Phlegmariurus for signs of genetic discordance,which can provide valuable insight into the underlying causes of such conflict(e.g.,hybridization,incomplete lineage sorting,or horizontal gene transfer).We found strong evidence that two WGD events occurred along the phylogenetic backbone of Lycopodiaceae,with one occurring in the common ancestor of extant Phlegmariurus(Lycopodiaceae)approximately 22-23 million years ago(Mya)and the other occurring in the common ancestor of Lycopodiaceae around 206-214 Mya.Interestingly,we found significant genetic discordance in the genus Phlegmariurus,indicating that the genus has a complex evolutionary history.This study provides molecular evidence for multiple WGDs in Lycopodiaceae and offers phylogenetic clues to the evolutionary history of Lycopodiaceae.

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

Gene duplications provide evolutionary potentials for generating novel functions, while polyploidization or whole genome duplication （WGD） doubles the chromosomes initially and results in hundreds to thousands of retained duplicates. WGDs are strongly supported by evidence commonly found in many species-rich lineages of eukaryotes, and thus are considered as a major driving force in species diversification. We per- formed comparative genomic and phylogenomic analyses of 59 public genomes/transcriptomes and 46 newly sequenced transcriptomes covering major lineages of angiosperms to detect large-scale gene dupli- cation events by surveying tens of thousands of gene family trees. These analyses confirmed most of the previously reported WGDs and provided strong evidence for novel ones in many lineages. The detected WGDs supported a model of exponential gene loss during evolution with an estimated half-life of approx- imately 21.6 million years, and were correlated with both the emergence of lineages with high degrees of diversification and periods of global climate changes. The new datasets and analyses detected many novel WGDs widely spread during angiosperm evolution, uncovered preferential retention of gene functions in essential cellular metabolisms, and provided clues for the roles of WGD in promoting angiosperm radiation and enhancing their adaptation to environmental changes.

Phylotranscriptomics in Cucurbitaceae Reveal Multiple Whole-Genome Duplications and Key Morphological and Molecular Innovations

The ability of climbing plants to grow upward along others to reach the canopy for photosynthesis is hypothesized as a key innovation in flowering plants.Most members of the Cucurbitaceae,a family containing^1000 species and many important crops,are climbers and have characteristic tendrils and pepo fruits.Here,we present 127 newly sequenced transcdptomes and genomes along with other datasets for a total of 136 cucurbits representing all tribes to establish a robust Cucurbitaceae phylogeny containing eight highly resolved major clades.We analyzed whole-genome duplication,diversification dynamics,and ancestral morphologies,and found that after early genome duplication event(s),a burst of diversification and morphological innovations in flower,fruit,and root characters occurred under the climate optimum in the Early Eocene.Species radiation during the Mid-Eocene Climatic Optimum also coincided with several morphological changes shared by 80%of cucurbits.We found that the cucurbit-specific tendril identity gene TEN originated from a paleo-polyploidization event at the origin of the family.Our results support the hypothesis that cucurbit diversifications were probably driven by increased genetic diversity following polyploidizations and by trait morphological innovations under paleo-climate upheavals.Our study provides a phylogenetic framework and new insights into morphological and genomic changes underlying the adaptive evolution of Cucurbitaceae.

Functional Divergence between Subgenomes anc Gene Pairs after Whole Genome Duplications

Gene loss following whole genome duplication （WGD） is often biased, with one subgenome retaining more ancestral genes and the other sustaining more gene deletions. While bias toward the greater expression of gene copies on one subgenome can explain bias in gene loss, this raises the question to what drives differences in gene expression levels between subgenomes. Differences in chromatin modifications and epigenetic markers between subgenomes in several model species are now being identified, providing an explanation for bias in gene expression between subgenomes. WGDs can be classified into duplications with higher, biased gene loss and bias in gene expression between subgenomes versus those with lower, unbiased rates of gene loss and an absence of detectable bias between subgenomes; however, the origi- nally proposed link between these two classes and whether WGD results from an allo- or autopolyploid event is inconsistent with recent data from the allopolyploid Capsella bursa-pastoris. The gene balance hypothesis can explain bias in the functional categories of genes retained following WGD, the difference in gene loss rates between unbiased and biased WGDs, and how plant genomes have avoided being overrun with genes encoding dose-sensitive subunits of multiprotein complexes. Comparisons of gene expression patterns between retained transcription factor pairs in maize suggest the high degree of retention for WGD-derived pairs of transcription factors may instead be explained by the older duplication-degeneration-complementation model.

Recent genome duplications facilitate the phenotypic diversity of Hb repertoire in the Cyprinidae

Whole-genome duplications(WGDs)are an important contributor to phenotypic innovations in evolutionary history.The diversity of blood oxygen transport traits is the perfect reflection of physiological versatility for evolutionary success among vertebrates.In this study,the evolutionary changes of hemoglobin(Hb)repertoire driven by the recent genome duplications were detected in representative Cyprinidae fish,including eight diploid and four tetraploid species.Comparative genomic analysis revealed a substantial variation in both membership composition and intragenomic organization of Hb genes in these species.Phylogenetic reconstruction analyses were conducted to characterize the evolutionary history of these genes.Data were integrated with the expression profiles of the genes during ontogeny.Our results indicated that genome duplications facilitated the phenotypic diversity of the Hb gene family;each was associated with species-specific changes in gene content via gene loss and fusion after genome duplications.This led to repeated evolutionary transitions in the ontogenic regulation of Hb gene expression.Our results revealed that genome duplications helped to generate phenotypic changes in Cyprinidae Hb systems.

Whole Genome Duplication of Intra- and Inter-chromosomes in the Tomato Genome

Whole genome duplication （WGD） events have been proven to occur in the evolutionary history of most angiosperms. Tomato is considered a model species of the Solanaceae family. In this study, we describe the details of the evolutionary process of the tomato genome by detecting collinearity blocks and dating the WGD events on the tree of life by combining two different methods： synonymous substitution rates （Ks） and phylogenetic trees. In total, 593 collinearity blocks were discovered out of 12 pseudo-chromosomes con- structed. It was evident that chromosome 2 had experienced an intra-chromosomat duplication event. Major inter-chromosomal dupli- cation occurred among all the pseudo-chromosome. We calculated the Ks value of these collinearity blocks. Two peaks of Ks distribution were found, corresponding to two WGD events occurring approximately 36-82 million years ago （MYA） and 148--205 MYA. Additionally, the results of phylogenetic trees suggested that the more recent WGD event may have occurred after the divergence of the rosidasterid clade, but before the major diversification in Solanaceae. The older WGD event was shown to have occurred before the divergence of the rosid-asterid clade and after the divergence of rice-Arabidopsis （monocot-dicot）.

Genome evolution trend of common carp (Cyprinus carpio L.) as revealed by the analysis of microsatellite loci in a gynogentic family

Genome evolution arises from two main ways of duplication and reduction. Fish specific genome duplication （FSGD） may have occurred before the radiation of the teleosts. Common carp （Cyprinus carpio L.） has been considered to be a tetraploid species, because of its chromosome numbers （2n=100） and its high DNA content. Using 69 microsatellite primer pairs, the variations were studied to better understand the genome evolution （genome duplication and diploidization） of common carp from a gynogenetic family. About 48% of primer pairs were estimated to amplify duplicates based on the number of PCR amplification per individual. Segregation patterns in the family suggested a partially duplicated genome structure and disomic inheritance. This indicates that the common carp is tetraploid and polyploidy occurred by allotetraploidy. Two primer pairs （HLJ021 and HLJ332） were estimated to amplify reduction based on the number of PCR amplification per individual. One allele in HLJ002 locus and HLJ332 locus was clearly lost in the gynogenetic family and the same as in six wild populations. Segregation patterns in the family suggested a partially diplodization genome structure. A hypothesis transition （dynamic） and equilibrium （static） were proposed to explain the common carp genome evolution between genome duplication and diploidization.

The impact of tandem duplication on gene evolution in Solanaceae species

Whole genome duplication(WGD) and tandem duplication(TD) are important modes of gene amplification and functional innovation, and they are common in plant genome evolution. We analyzed the genomes of three Solanaceae species(Solanum lycopersicum, Capsicum annuum, and Petunia inflata), which share a common distant ancestor with Vitis vinifera, Theobroma cacao, and Coffea canephora but have undergone an extra whole genome triplication(WGT) event. The analysis was used to investigate the phenomenon of tandem gene evolution with(S. lycopersicum) or without WGT(V. vinifera). Among the tandem gene arrays in these genomes, we found that V. vinifera, which has not experienced the WGT event, retained relatively more and larger tandem duplicated gene(TDG) clusters than the Solanaceae species that experienced the WGT event. Larger TDG clusters tend to be derived from older TD events, so this indicates that continuous TDGs(absolute dosage) accumulated during long-term evolution. In addition, WGD and TD show a significant bias in the functional categories of the genes retained. WGD tends to retain dose-sensitive genes related to biological processes, including DNA-binding and transcription factor activity, while TD tends to retain genes involved in stress resistance. WGD and TD also provide more possibilities for gene functional innovation through gene fusion and fission. The TDG cluster containing the tomato fusarium wilt resistance gene I3 contains 15 genes, and one of these genes, Solyc07g055560, has undergone a fusion event after the duplication events. These data provide evidence that helps explain the new functionalization of TDGs in adapting to environmental changes.

Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution,lignin biosynthesis regulation,and stress tolerance

Durian(Durio zibethinus)is a tropical fruit that has a unique flavor and aroma.It occupies a significant phylogenetic position within the Malvaceae family.Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling,resulting in an abundant genomic diversity.However,the ancestral karyotypes of the Malvaceae family,as well as the evolution trajectory leading to the28 chromosomes in durian,remain poorly understood.Here,we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses.By analyzing the collinear blocks between cacao and durian,we inferred 11 Malvaceae ancestral karyotypes.These blocks were present in a single-copy form in cacao and mainly in triplicates in durian,possibly resulting from a recent whole genome triplication(WGT)event that led to hexaploidization of the durian genome around 20(17–24)million years ago.A large proportion of the duplicated genes in durian,such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis,are derived directly from whole genome duplication,which makes it an important force in reshaping its genomic architecture.Transcriptome studies have revealed that genes involved in feruloyl-Co A formations were highly preferentially expressed in fruit peels,indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins.Among all the analyzed transcription factors(TFs),members of the heat shock factor family(HSF)were the most significantly upregulated under heat stress.All subfamilies of genes encoding heat shock proteins(HSPs)in the durian genome appear to have undergone expansion.The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified.Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome.We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.

Comparative DNA-methylome and transcriptome analysis reveals heterosis-and polyploidy-associated epigenetic changes in rice

Heterosis and polyploidy have an overwhelming influence on plant evolution.Recently,polyploid rice hybrids have been used to breed new rice varieties because they combine the advantages of both heterosis and polyploidy.In this study,we generated six rice lines:autotetraploid rice hybrids and their autotetraploid parents,diploid donors,and hybrids of the diploid donors.To investigate the molecular mechanism controlling the effects of both hybridization and polyploidization,we performed bisulfite and RNA sequencing on young panicles at the pollen meiosis stage to compare the DNA metabolomes and transcriptomes among the six rice lines.The hybrids lines were hypermethylated compared to their corresponding parents and the autotetraploid lines showed globally increased DNA methylation of their transposable elements compared to the diploid donors.The alteration in DNA methylation level corresponded to the differential gene expressions among the rice genotypes,suggesting that methylation changes induced by polyploidization and hybridization may affect gene expression.Groups of gene candidates were identified that may be associated with heterosis and polyploidy.Our results provide DNA information that can be used to investigate epigenetic modification during heterosis and polyploidy in rice.

Genomic organization and evolution of ruminant lysozyme c genes

Ruminant stomach lysozyme is a long established model of adaptive gene evolution. Evolution of stomach lysozyme function required changes in the site of expression of the lysozyme c gene and changes in the enzymatic properties of the enzyme. In ruminant mammals, these changes were associated with a change in the size of the lysozyme c gene family. The recent release of near complete genome sequences from several ruminant species allows a more complete examination of the evolution and diversification of the lysozyme c gene family. Here we characterize the size of the lysozyme c gene family in extant ruminants and demonstrate that their pecoran ruminant ancestor had a family of at least 10 lysozyme c genes, which included at least two pseudogenes. Evolutionary analysis of the ruminant lysozyme c gene sequences demonstrate that each of the four exons of the lysozyme c gene has a unique evolutionary history, indicating that they participated independently in concerted evolution. These analyses also show that episodic changes in the evolutionary constraints on the protein sequences occurred, with lysozyme c genes expressed in the abomasum of the stomach of extant ruminant species showing the greatest levels of selective constraints.

The Tartary Buckwheat Genome Provides Insights into Rutin Biosynthesis and Abiotic Stress Tolerance

Tartary buckwheat （Fagopyrum tataricum） is an important pseudocereal crop that is strongly adapted to growth in adverse environments. Its gluten-free grain contains complete proteins with a well-balanced composition of essential amino acids and is a rich source of beneficial phytochemicals that provide significant health benefits. Here, we report a high-quality, chromosome-scale Tartary buckwheat genome sequence of- 489.3 Mb that is assembled by combining whole-genome shotgun sequencing of both Illumina short reads and single-molecule real-time long reads, sequence tags of a large DNA insert fosmid library, Hi-C sequencing data, and BioNano genome maps. We annotated 33 366 high-confidence protein-coding genes based on expression evidence. Comparisons of the intra-genome with the sugar beet genome revealed an independent whole-genome duplication that occurred in the buckwheat lineage after they diverged from the common ancestor, which was not shared with rosids or asterids. The reference genome facilitated the identification of many new genes predicted to be involved in rutin biosynthesis and regulation, aluminum stress resistance, and in drought and cold stress responses. Our data suggest that Tartary buckwheat＇s ability to tolerate high levels of abiotic stress is attributed to the expansion of several gene families involved in signal transduction, gene regulation, and membrane transport. The availability of these genomic resources will facilitate the discovery of agronomically and nutritionally important genes and genetic improvement of Tartary buckwheat.

Hox Gene Clusters of Early Vertebrates:Do They Serve as Reliable Markers for Genome Evolution?

Hox genes, responsible for regional specification along the anteroposterior axis in embryogenesis, are found as clusters in most eumetazoan genomes sequenced to date. Invertebrates possess a single Hox gene cluster with some exceptions of secondary cluster breakages, while osteichthyans （bony vertebrates） have multiple Hox clusters. In tetrapods, four Hox clusters, derived from the so-called two-round whole genome duplications （2R-WGDs）, are observed. Overall, the number of Hox gene clusters has been regarded as a reliable marker of ploidy levels in animal genomes. In fact, this scheme also fits the situations in teleost fishes that experienced an additional WGD. In this review, I focus on cyclostomes and cartilaginous fishes as lineages that would fill the gap between invertebrates and osteichthyans. A recent study highlighted a possible loss of the HoxC cluster in the galeomorph shark lineage, while other aspects of cartilaginous fish Hox clusters usually mark their conserved nature. In contrast, existing resources suggest that the cyclostomes exhibit a different mode of Hox cluster organization. For this group of species, whose genomes could have differently responded to the 2R-WGDs from jawed vertebrates, therefore the number of Hox clusters may not serve as a good indicator of their ploidy level.

Improved genome assembly of Chinese sucker(Myxocyprinus asiaticus)provides insights into the identification and characterization of pharyngeal teeth related maker genes in Cyprinoidei

The Chinese sucker,Myxocyprinus asiaticus(M.asiaticus,Catostomidae,Cypriniformes),is the only living species of Catostomidae in Asia.There are more than 75 species of this family in North America.The fossil record of this group dates back to the early Eocene.As the Chinese sucker is located at the base of the Cyprinoidei phylogeny,this species is also important in clarifying the evolutionary relationships within Cyprinoidei.Here,we assembled a high-quality genome of the Chinese sucker,contig N50(40.26 Mb),which is nearly ten times longer than the previous version(4.19 Mb).Phylogenetic analysis identified that Chinese sucker together with Cyprinidae groups are paraphyletic with respect to Cobitoidea.The specific whole genome duplication event of the Chinese sucker was estimated to have occurred~25.9 million years ago.Analysis of population historical changes indicated a trend of reduction for the Chinese sucker and T.tibetana.Since Dlx genes play a key role in Cypriniformes pharyngeal teeth development,we conducted a genome-wide identification of Dlx genes,and found that these genes were doubled in whole genome duplication events,followed by the loss of specific copies.Transcriptome results showed that the expression levels of these paralogous genes were similar.This genomic resource provides useful information for the protection of Chinese sucker and functional study of Dlx genes.

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.

Polyploid organisms

Polyploids are organisms with three or more complete chromosome sets. Polyploidization is widespread in plants and animals, and is an important mechanism of speciation. Genome sequencing and related molecular systematics and bioinformatics studies on plants and animals in recent years support the view that species have been shaped by whole genome duplication during evolution. The stability of polyploids depends on rapid genome recombination and changes in gene expression after formation. The formation of polyploids and subsequent diploidization are important aspects in long-term evolution. Polyploids can be formed in various ways. Among them, hybrid organisms formed by distant hybridization could produce unreduced gametes and thus generate offspring with doubled chromosomes, which is a fast, efficient method of polyploidization. The formation of fertile polyploids not only promoted the interflow of genetic materials among species and enriched the species diversity, but also laid the foundation for polyploidy breeding. The study of polyploids has both important theoretical significance and valuable applications. The production and application of polyploidy breeding have brought remarkable economic and social benefits.

Innovations and stepwise evolution of CBFs/DREB1s and their regulatory networks in angiosperms

The C-repeat binding factors/dehydrationresponsive element binding protein 1 s(CBFs/DREB1 s)have been identified as major regulators of cold acclimation in many angiosperm plants.However,their origin and evolutionary process associated to cold responsiveness are still lacking.By integrating multi-omics data of genomes,transcriptomes,and CBFs/DREB1 s genome-wide binding profiles,we unveil the origin and evolution of CBFs/DREB1 s and their regulatory network.Gene collinearity and phylogeny analyses show that CBF/DREB1 is an innovation evolved from tandem duplication-derived DREBⅢgene.A subsequent event of e-whole genome duplication led to two CBF/DREB1 archetypes(CladesⅠandⅡ)in ancient angiosperms.In contrast to cold-insensitivity of Clade I and their parent DREBⅢgenes,CladeⅡevolved a further innovation in cold-sensitive response and was stepwise expanded in eudicots and monocots by independent duplications.In geological time,the duplication events were mainly enriched around the Cretaceous-Paleogene(K-Pg)boundary and/or in the Late Cenozoic Ice Age,when the global average temperature significantly decreased.Consequently,the duplicated CBF/DREB1 genes contributed to the rewiring of CBFs/DREB1 s-regulatory network for cold tolerance.Altogether,our results highlight an origin and convergent evolution of CBFs/DREB1 s and their regulatory network probably for angiosperms adaptation to global cooling.

Unlocking plant metabolic diversity: A (pan)- genomic view

Plants produce a remarkable diversity of structurally and functionally diverse natural chemicals that serve as adaptive compounds throughout their life cycles.However,unlocking this metabolic diversity is significantly impeded by the size,complexity,and abundant repetitive elements of typical plant genomes.As genome sequencing becomes routine,we anticipate that links between metabolic diversity and genetic variation will be strengthened.In addition,an ever-increasing number of plant genomes have revealed that biosynthetic gene clusters are not only a hallmark of microbes and fungi;gene clusters for various classes of compounds have also been found in plants,and many are associated with important agronomic traits.We present recent examples of plant metabolic diversification that have been discovered through the exploration and exploitation of various genomic and pan-genomic data.We also draw attention to the fundamental genomic and pan-genomic basis of plant chemodiversity and discuss challenges and future perspectives for investigating metabolic diversity in the coming pan-genomics era.