Small-Scale Duplications Play a Significant Role in Rice Genome Evolution

Genes are continually being created by the processes of genome duplication （ohnolog） and gene duplication （paralog）. Whole-genome duplications have been found to be widespread in plant species and play an important role in plant evolution. Clearly un-overlapping duplicated blocks of whole-genome duplications can be detected in the genome of sequenced rice （Oryza sativa）. Syntenic ohnolog pairs （ohnologues） of the whole-genome duplications in rice were identified based on their syntenic duplicate lines. The paralogs of ohnologues were further scanned using multi-round reciprocal BLAST best-hit searching （E〈e^-14）. The results indicated that an average of 0.55 sister paralogs could be found for every ohnologue in rice. These results suggest that small-scale duplications, as well as whole-genome duplications, play a significant role in the two duplicated rice genomes.

The chromosome-level genome of double-petal phenotype jasmine provides insights into the biosynthesis of floral scent

Jasmine(Jasminum sambac Aiton)is a well-known cultivated plant species for its fragrant flowers used in the perfume industry and cosmetics.However,the genetic basis of its floral scent is largely unknown.In this study,using PacBio,Illumina,10×Genomics and highthroughput chromosome conformation capture(Hi-C)sequencing technologies,a high-quality chromosome-level reference genome for J.sambac was obtained,exploiting a double-petal phenotype cultivar‘Shuangbanmoli’(JSSB).The results showed that the final assembled genome of JSSB is 580.33 Mb in size(contig N50=1.05 Mb;scaffold N50=45.07 Mb)with a total of 39618 predicted protein-coding genes.Our analyses revealed that the JSSB genome has undergone an ancient whole-genome duplication(WGD)event at 91.68 million years ago(Mya).It was estimated that J.sambac diverged from the lineage leading to Olea europaea and Osmanthus fragrans about 28.8 Mya.On the basis of a combination of genomic,transcriptomic and metabolomic analyses,a range of floral scent volatiles and genes were identified involved in the benzenoid/phenylpropanoid and terpenoid biosynthesis pathways.The results provide new insights into the molecular mechanism of its fragrance biosynthesis in jasmine.

The Reference Genome of Tea Plant and Resequencing of 81 Diverse Accessions Provide Insights into Its Genome Evolution and Adaptation

Tea plant is an important economic crop,which is used to produce the world's oldest and most widely consumed tea beverages.Here,we present a high-quality reference genome assembly of the tea plant(Camellia sinensis var.sinensis)consisting of 15 pseudo-chromosomes.LTR retrotransposons(LTR-RTs)account for 70.38%of the genome,and we present evidence that LTR-RTS play critical roles in genome size expansion and the transcriptional diversification of tea plant genes through preferential insertion in promoter regions and introns.Genes,particularly those coding for terpene biosynthesis pro-teins,associated with tea aroma and stress resistance were significantly amplified through recent tandem duplications and exist as gene clusters in tea plant genome.Phylogenetic analysis of the sequences of 81 tea plant accessions with diverse origins revealed three well-differentiated tea plant populations,support-ing the proposition for the southwest origin of the Chinese cultivated tea plant and its later spread to western Asia through introduction.Domestication and modern breeding left significant signatures on hundreds of genes in the tea plant genome,particularly those associated with tea quality and stress resis-tance.The genomic sequences of the reported reference and resequenced tea plant accessions provide valuable resources for future functional genomics study and molecular breeding of improved cul-tivars of tea plants.

A Chromosome-Level Genome Assembly of Garlic (Allium sativum) Provides Insights into Genome Evolution and Allicin Biosynthesis

Garlic,an economically important vegetable,spice,and medicinal crop,produces highly enlarged bulbs and unique organosulfur compounds.Here,we report a chromosome-level genome assembly for garlic,with a total size of approximately 16.24 Gb,as well as the annotation of 57561 predicted protein-coding genes,making garlic the first Allium species with a sequenced genome.Analysis of this garlic genome assembly reveals a recent burst of transposable elements,explaining the substantial expansion of the garlic genome.We examined the evolution of certain genes associated with the biosynthesis of allicin and inulin neoseries-type fructans,and provided new insights into the biosynthesis of these two compounds.Furthermore,a large-scale transcriptome was produced to characterize the expression patterns of garlic genes in different tissues and at various growth stages of enlarged bulbs.The reference genome and large-scale transcriptome data generated in this study provide valuable new resources for research on garlic biology and breeding.

Transposable elements play an important role during cotton genome evolution and fiber cell development

Transposable elements(TEs)usually occupy largest fractions of plant genome and are also the most variable part of the structure.Although traditionally it is hallmarked as"junk and selfish DNA",today more and more evidence points out TE’s participation in gene regulations including gene mutation,duplication,movement and novel gene creation via genetic and epigenetic mechanisms.The recently sequenced genomes of diploid cottons Gossypium arboreum(AA)and Gossypium raimondii(DD)together with their allotetraploid progeny Gossypium hirsutum(At At Dt Dt)provides a unique opportunity to compare genome variations in the Gossypium genus and to analyze the functions of TEs during its evolution.TEs accounted for 57%,68.5%and67.2%,respectively in DD,AA and At At Dt Dt genomes.The 1,694 Mb A-genome was found to harbor more LTR(long terminal repeat)-type retrotransposons that made cardinal contributions to the twofold increase in its genome size after evolution from the 775.2 Mb D-genome.Although the 2,173 Mb At At Dt Dt genome showed similar TE content to the A-genome,the total numbers of LTR-gypsy and LTR-copia type TEs varied significantly between these two genomes.Considering their roles on rewiring gene regulatory networks,we believe that TEs may somehow be involved in cotton fiber cell development.Indeed,the insertion or deletion of different TEs in the upstream region of two important transcription factor genes in At or Dt subgenomes resulted in qualitative differences in target gene expression.We suggest that our findings may open a window for improving cotton agronomic traits by editing TE activities.

Rapid genomic changes in polyploid wheat and related species:implications for genome evolution and genetic improvement

A polyploid organism by possessing more than two sets of chromosomes from one species （autopolyploidy） or two or more species （allopolyploidy） is known to have evolutionary advantages. However, by what means a polyploid accommodates increased genetic dosage or divergent genomes （allopolyploidy） in one cell nucleus and cytoplasm constitutes an enormous challenge. Recent years have witnessed efforts and progress in exploring the possible mechanisms by which these seemingly intangible hurdles of polyploidy may be ameliorated or eventually overcome. In particular, the documentation of rapid and extensive non-Mendelian genetic and epigenetic changes that often accompany nascent polyploidy is revealing： the resulting non-additive and novel gene expression at global, regional and local levels, and timely restoration of meiotic chromosomal behavior towards bivalent pairing and disomic inheritance may ensure rapid establishment and stabilization as well as its long-term evolutionary success. Further elucidation on these novel mechanisms underpinning polyploidy will promote our understanding on fundamental issues in evolutionary biology and in our manipulation capacities in future genetic improvement of important crops that are currently polyploids in genomic constitution. This review is intended to provide an updated discussion on these interesting and important issues within the scope of a specific yet one of the most important plant groups--polyploid wheat and its related species.

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.

Genome and population evolution and environmental adaptation of Glyptosternon maculatum on the Qinghai-Tibet Plateau

Persistent uplift means the Qinghai-Tibet Plateau(QTP)is an ideal natural laboratory to investigate genome evolution and adaptation within highland environments.However,how paleogeographic and paleoclimatic events influence the genome and population of endemic fish species remains unclear.Glyptosternon maculatum is an ancient endemic fish found on the QTP and the only critically endangered species in the Sisoridae family.Here,we found that major transposons in the G.maculatum genome showed episodic bursts,consistent with contemporaneous geological and climatic events during the QTP formation.Notably,histone genes showed significant expansion in the G.maculatum genome,which may be mediated by long interspersed nuclear elements(LINE)repetitive element duplications.Population analysis showed that ancestral G.maculatum populations experienced two significant depressions 2.6 million years ago(Mya)and 10000 years ago,exhibiting excellent synchronization with Quaternary glaciation and the Younger Dryas,respectively.Thus,we propose that paleogeography and paleoclimate were dominating driving forces for population dynamics in endemic fish on the QTP.Tectonic movements and temperature fluctuation likely destroyed the habitat and disrupted the drainage connectivity among populations.These factors may have caused severe bottlenecks and limited migration among ancestral G.maculatum populations,resulting in the low genetic diversity and endangered status of the species today.

Cotton functional genomics reveals global insight into genome evolution and fiber development

Due to the economic value of natural textile fiber, cotton has attracted much research attention, which has led to the publication of two diploid genomes and two tetraploid genomes. These big data facilitate functional genomic study in cotton, and allow researchers to investigate cotton genome structure, gene expression, and protein function on the global scale using high-throughput methods. In this review, we summarized recent studies of cotton genomes. Population genomic analyses revealed the domestication history of cultivated upland cotton and the roles of transposable elements in cotton genome evolution.Alternative splicing of cotton transcriptomes was evaluated genome-widely. Several important gene families like MYC, NAC, Sus and GhPLDal were systematically identified and classified based on genetic structure and biological function. High-throughput proteomics also unraveled the key functional proteins correlated with fiber development. Functional genomic studies have provided unprecedented insights into global-scale methods for cotton research.

Au Elements and Their Evolution in Some AIIopolyploid Genomes of Aegilops

To study the sequences of short interspersed nuclear elements （SINEs） evolution in some allopolyploid genomes of Aegilops, 108 Au element fragments （a novel kind of plant SINE） were amplified and sequenced in 10 species of Aegilops, which were clustered into three different groups （A, B and C） based on their related geuome types. The sequences of these Au element fragments were heterogouous in di-, tetra-, and hexa-ploids, and the deudrograms of Au element obtained from phylogenetic analysis were very complex in each group and could be clustered into 15, 15 and 22 families, respectively. In this study, three rules about Au elements evolution have been drawn from the results： i. Most families were composed of Au element members with different host species in three groups; ii. Family 1-6 in Group A, Family 1-6 in Group B, Family 1-4 and Family 6-13 in Group C contained only one, apparently highly degenerate Au dement member （a single representative elemeut）; iii. Elements generally fell into clades that were species-specific with respect to their host species. The potential mechanisms of Au element evolution in Aegilops were discussed.

High-quality genomes of Bombax ceiba and Ceiba pentandra provide insights into the evolution of Malvaceae species and differences in their natural fiber development

Members of the Malvaceae family,including Corchorus spp.,Gossypium spp.,Bombax spp.,and Ceiba spp.,are important sources of naturalfibers.In the past decade,the genomes of several Malvaceae species have been assembled;however,the evolutionary history of Malvaceae species and the differences in theirfiber development remain to be clarified.Here,we report the genome assembly and annotation of two nat-uralfiber plants from the Malvaceae,Bombax ceiba and Ceiba pentandra,whose assembled genome sizes are 783.56 Mb and 1575.47 Mb,respectively.Comparative analysis revealed that whole-genome duplication and Gypsy long terminal repeat retroelements have been the major causes of differences in chromosome number(2n=14 to 2n=96)and genome size(234 Mb to 2676 Mb)among Malvaceae species.We also used comparative genomic analyses to reconstruct the ancestral Malvaceae karyotype with 11 proto-chromo-somes,providing new insights into the evolutionary trajectories of Malvaceae species.MYB-MIXTA-like 3 is relatively conserved among the Malvaceae and functions infiber cell-fate determination in the epidermis.It appears to perform this function in any tissue where it is expressed,i.e.infibers on the endo-carp of B.ceiba and in ovulefibers of cotton.We identified a structural variation in a cellulose synthase gene and a higher copy number of cellulose synthase-like genes as possible causes of thefiner,less spinnable,weakerfibers of B.ceiba.Our study provides two high-quality genomes of naturalfiber plants and offers insights into the evolution of Malvaceae species and differences in their naturalfiber formation and devel-opment through multi-omics analysis.

A reference-grade genome of the xerophyte Ammopiptanthus mongolicus sheds light on its evolution history in legumes and droughttolerance mechanisms

Plants that grow in extreme environments represent unique sources of stress-resistance genes and mechanisms.Ammopiptanthus mongolicus(Leguminosae)is a xerophytic evergreen broadleaf shrub native to semi-arid and desert regions;however,its drought-tolerance mechanisms remain poorly understood.Here,we report the assembly of a reference-grade genome for A.mongolicus,describe its evolutionary history within the legume family,and examine its drought-tolerance mechanisms.The assembled genome is 843.07 Mb in length,with 98.7%of the sequences successfully anchored to the nine chromosomes of A.mongolicus.The genome is predicted to contain 47611 protein-coding genes,and 70.71%of the genome is composed of repetitive sequences;these are dominated by transposable elements,particularly longterminal-repeat retrotransposons.Evolutionary analyses revealed two whole-genome duplication(WGD)events at 130 and 58 million years ago(mya)that are shared by the genus Ammopiptanthus and other legumes,but no species-specific WGDs were found within this genus.Ancestral genome reconstruction revealed that the A.mongolicus genome has undergone fewer rearrangements than other genomes in the legume family,confirming its status as a"relict plant".Transcriptomic analyses demonstrated that genes involved in cuticular wax biosynthesis and transport are highly expressed,both under normal conditions and in response to polyethylene glycol-induced dehydration.Significant induction of genes related to ethylene biosynthesis and signaling was also observed in leaves under dehydration stress,suggesting that enhanced ethylene response and formation of thick waxy cuticles are two major mechanisms of drought tolerance in A.mongolicus.Ectopic expression of AmERF2,an ethylene response factor unique to A.mongolicus,can markedly increase the drought tolerance of transgenic Arabidopsis thaliana plants,demonstrating the potential for application of A.mongolicus genes in crop improvement.

Molecular evolution of the rice miR395 gene family

MicroRNAs (miRNAs) are 20-22 nucleotide non-coding RNAs that play important roles in plant and animal development. They are usually processed from larger precursors that can form stem-loop structures. Among 20 miRNA families that are conserved between Arabidopsis and rice, the rice miR395 gene family was unique because it was organized into compact clusters that could be transcribed as one single transcript. We show here that in fact this family had four clusters of total 24 genes. Three of these clusters were segmental duplications. They contained miR395 genes of both 120 bp and 66 bp long. However, only the latter was repeatedly duplicated. The fourth cluster contained miR395 genes of two different sizes that could be the consequences of intergenic recombination of genes from the first three clusters. On each cluster, both 1-duplication and 2-duplication histories were observed based on the sequence similarity between miR395 genes, some of which were nearly identical suggesting a recent origin. This was supported by a miR395 locus survey among several species of the genus Oryza, where two clusters were only found in species with an AA genome, the genome of the cultivated rice. A comparative study of the genomic organization of Medicago truncatula miR395 gene family showed significant expansion of intergenic spaces indicating that the originally clustered genes were drifting away from each other. The diverse genomic organizations of a conserved microRNA gene family in different plant genomes indicated that this important negative gene regulation system has undergone dramatic tune-ups in plant genomes.

Science Letters:Two ancient rounds of polyploidy in rice genome

An ancient genome duplication (PPP1) that predates divergence of the cereals has recently been recognized. We report here another potentially older large-scale duplication (PPP2) event that predates monocot-dicot divergence in the genome of rice (Oryza sativa L.), as inferred from the age distribution of pairs of duplicate genes based on recent genome data for rice. Our results suggest that paleopolyploidy was widespread and played an important role in the evolution of rice.

Genomic Evolution and Variation of SARS-CoV-2 in the Early Phase of COVID-19 Pandemic in Guangdong Province,China

Severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)with unknown origin spread rapidly to 222 countries,areas or territories.To investigate the genomic evolution and variation in the early phase of COVID-19 pandemic in Guangdong,60 specimens of SARS-CoV-2 were used to perform whole genome sequencing,and genomics,amino acid variation and Spike protein structure modeling analyses.Phylogenetic analysis suggested that the early variation in the SARS-CoV-2 genome was still intra-species,with no evolution to other coronaviruses.There were one to seven nucleotide variations(SNVs)in each genome and all SNVs were distributed in various fragments of the genome.The Spike protein bound with human receptor,an amino acid salt bridge and a potential furin cleavage site were found in the SARS-CoV-2 using molecular modeling.Our study clarifed the characteristics of SARS-CoV-2 genomic evolution,variation and Spike protein structure in the early phase of local cases in Guangdong,which provided reference for generating prevention and control strategies and tracing the source of new outbreaks.

Genome assembly of the Brassicaceae diploid Orychophragmus violaceus reveals complex whole-genome duplication and evolution of dihydroxy fatty acid metabolism

Orychophragmus violaceus is a Brassicaceae species widely cultivated in China,particularly as a winter cover crop in northern China because of its low-temperature tolerance and low water demand.Recently,O.violaceus has also been cultivated as a potential industrial oilseed crop because of its abundant 24-carbon dihydroxy fatty acids(diOH-FAs),which contribute to superior high-temperature lubricant properties.In this study,we performed de novo assembly of the O.violaceus genome.Whole-genome synteny analysis of the genomes of its relatives demonstrated that O.violaceus is a diploid that has undergone an extrawhole-genome duplication(WGD)after the Brassicaceae-specific a-WGD event,with a basic chromosome number of x=12.Formation of diOH-FAs is hypothesized to have occurred after the WGD event.Based on the genome and the transcriptome data from multiple stages of seed development,we predicted that OvDGAT1-1 and OvDGAT1-2 are candidate genes for the regulation of diOH-FA storage in O.violaceus seeds.These results may greatly facilitate the development of heat-tolerant and eco-friendly plant-based lubricants using O.violaceus seed oil and improve our understanding of the genomic evolution of Brassicaceae.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies.Poplars,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental adaptability.In this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation.Through the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body regions.Further comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence.We have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration formation.Finally,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://www.populus-superpangenome.com).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

A chromosome-level genome assembly of the miiuy croaker(Miichthys miiuy)using nanopore sequencing and Hi-C

Miiuy croaker,Miichthys miiuy is an ecologically important teleost species which is widely distributed in southeast coast of China.In this study,we present a chromosomal-scale genome assembly of the miiuy croaker which is an important Sciaenidae fish and economical species.We adopted Oxford Nanopore and Hi-C sequencing techniques to achieve an assembly with high accuracy and completeness.The investigation of genome characteristic and functional features may provide insights into the study of phylogenetic diversity of miiuy croaker.This study can also be beneficial to improve molecular assisted breeding techniques.Moreover,it can be a great resource to better conduct further study of other sciaenids.

Study on Genomic Changes in Partial Amphiploids of Common Wheat_Wheatgrass

According to conventional theory, little genomic changes should occur in homozygous and stable amphiploids of the grass family, particularly those involving polyploid wheat as a parent. In the present study, however, extensive genomic changes were detected in two octoploid partial amphiploids of common wheat (Triticum aestivum L.)_wheatgrass (Agropyron intermedium (Host) P.B.=Elytrigia intermedia (Host) Nevski=Thinopyrum intermedium (Host) Barkworth and Dewey), namely Zhong 3 and Zhong 5, by RFLP analysis using 10 low_copy, wheat chromosome_specific sequences and 33 representative homoeologous group_specific sequences as probes. Genomic changes involved loss of wheat hybridization fragment(s) and/or acquisition of new fragment(s). Uniformity of the RFLP patterns among 5 individual plants taken respectively from Zhong 3 and Zhong 5 in two successive generations, suggested that genomic changes probably had occurred in the early few generations after octoploid amphiploid formation, and remained essentially static thereafter. The highly similar RFLP patterns between Zhong 3 and Zhong 5, which had identical genomic constitution but differed from each other due to involvement of different wheat varieties as parents imply that genomic changes were probably not at random. Possible causes for the extensive and rapid genomic changes in the newly formed plant amphiploids, as well as their implications for polyploid genome evolution and breeding application are discussed.

Characterization of Two Groups of Low_copy and Specific DNA Sequences Isolated from Chromosome 7B of Common Wheat

Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play a critical role in the stabilization and establishment of nascent plant polyploids as new species. To further study this issue, five wheat chromosome 7B_specific sequences, isolated from common wheat (Triticum aestivum L.) by chromosome microdissection, were characterized. The sequences were studied by genomic Southern hybridizations on a collection of polyploid wheats and their diploid progenitors. Four sequences hybridized to all polyploid species, but at the diploid level to only species closely related to the B_genome of polyploid wheat. This indicates that these sequences originated with the divergence of the diploid species, and was then vertically transmitted to polyploids. One sequence hybridized to all species at both the diploid and polyploid levels, suggesting its elimination after the polyploid wheat formation. The hybridization of this sequence to two synthetic polyploid wheats indicated that sequence elimination is a rapid event and probably related to methylation status of the sequence. Based on the above results, we suggest that selective changes of low_copy sequences occur rapidly after polyploid formation, which may contribute to the differentiation of chromosomes in newly formed allopolyploid wheats.