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 pol...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.展开更多
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 functiona...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.展开更多
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 importan...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.展开更多
Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformat...Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.展开更多
The Malvaceae family,the most diverse family in the order Malvales,consists of nine subfamilies.Within the Firmiana genus of the Sterculioideae subfamily,most species are considered globally vulnerable,yet their genom...The Malvaceae family,the most diverse family in the order Malvales,consists of nine subfamilies.Within the Firmiana genus of the Sterculioideae subfamily,most species are considered globally vulnerable,yet their genomes remain unexplored.Here,we present a chromosome-level genome assembly for a representative Firmiana species,F.hainanensis,2n=40,totaling 1536 Mb.Phylogenomic analysis shows that F.hainanensis and Durio zibethinus have the closest evolutionary relationship,with an estimated divergence time of approximately 21 millions of years ago(MYA)and distinct polyploidization events in their histories.Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation(2n=14 to 2n=96).Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily(belonging to the Gypsy group)contributes to variation in genome size(ranging from 324 Mb to 1620 Mb).Additionally,genes associated with P450,peroxidase,and microtubules,and thereby related to cell wall biosynthesis,are significantly contracted in F.hainanensis,potentially leading to its lower wood density relative to Hopea hainanensis.Overall,our study provides insights into the evolution of chromosome number,genome size,and the genetic basis of cell wall biosynthesis in Malvaceae species.展开更多
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 sinensi...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.展开更多
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 ap...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.展开更多
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...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.展开更多
Tung tree(Vernicia fordii)is an economically important woody oil plant that produces tung oil rich in eleostearic acid.Here,we report a high-quality chromosome-scale genome sequence of tung tree.The genome sequence wa...Tung tree(Vernicia fordii)is an economically important woody oil plant that produces tung oil rich in eleostearic acid.Here,we report a high-quality chromosome-scale genome sequence of tung tree.The genome sequence was assembled by combining Illumina short reads,Pacific Biosciences single-molecule real-time long reads,and Hi-C sequencing data.The size of tung tree genome is 1.12 Gb,with 28,422 predicted genes and over 73%repeat sequences.The V.fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca.34.55 million years of evolutionary history of the tung tree lineage.Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms.The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance.Further,651 oil-related genes were identified,88 of which are predicted to be directly involved in tung oil biosynthesis.Relatively few phosphoenolpyruvate carboxykinase genes,and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed.The tung tree genome constitutes a valuable resource for understanding genome evolution,as well as for molecular breeding and genetic improvements for oil production.展开更多
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 inf...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.展开更多
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 rela...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.展开更多
Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly ...Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.展开更多
Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’spe...Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.展开更多
Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,199...Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).展开更多
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 s...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.展开更多
Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we develop...Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we developed a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualised the evolutionary trajectories of gene repeats.We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification modules.Results:This system delivered multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection.Inducing the toxin(RelE)expressing via a copper(II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin(RelB)module,resulting in~40 copies of a green fluorescence reporter gene per copy of genome.Copy-number changes,copy-number increase and copy-number decrease,and stable maintenance were visualised using the green fluorescence protein and blue chromoprotein AeBlue as reporters.Copy-number increases happened spontaneously and independent on a selection pressure.Increased copy number was quickly enriched through toxin-antitoxin-mediated selection.Conclusion:In summary,the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.展开更多
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 f...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.展开更多
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...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.展开更多
基金supported by the Program for Changjiang Scholars and Innovative Research Team (PCSIRT) in University in China (No. IRT0519)the National Natural Science Foundation of China (No. 30430060)
文摘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.
基金supported by the Natural Science Foundation of China(Nos.21602162 and 31690090)the National Science and Technology Major Project(No.2016ZX08005003-001)the Fundamental Research Funds for the Central Universities(No.104862016)
文摘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.
基金the National NaturalSciencc Foundation of China (90208022,30471067) IBM Shared University Research (LifeScience).
文摘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.
基金supported by the National Natural Science Foundation of China Project(Grant No.32260097)the National Guidance Foundation for Local Science and Technology Development of China(Grant No.[2023]009)the Natural Science Foundation for Distinguished Young Scholars of Hebei(Grant No.C2022209010)。
文摘Sechium edule(chayote)is an important vegetable crop belonging to the Cucurbitaceae family.To decipher the chayote genome,a highquality chromosome-level chayote genome was obtained by genome sequencing and bioinformatic analysis.The total length was612.91 Mb,and 25755 genes were detected in the chayote genome.The contig N50 was more than 20.01 Mb,and the scaffold N50 was over47.11 Mb.Of the genome,60.35%were composed of repetitive sequences,and 31.18%of genome sequences belonged to long-terminal repeats.A global alignment of homologous regions in chayote and other Cucurbitaceae plant genomes was constructed using grape as a reference.Based on this genome-wide and global alignment map,researchers can easily identify homologous collinear genes of the studied genomes in most Cucurbitaceae species.Twenty-five chayote accessions were divided into two subgroups based on phylogenetic tree,population structure analysis,and principal component analysis using genome re-sequencing data.The chayote genome,re-sequencing dataset,and comprehensive genomic analysis will accelerate comparative and functional genomic analysis of chayote and other Cucurbitaceae species in the future.
基金supported by the National Key R&D Program of China(2022YFF1001400)postdoctoral innovative talents support program(517000-X92308)+2 种基金the specific research fund of The Innovation Platform for Academicians of Hainan Province(YSPTZX202154,YSPTZX202139)the Research Startup Funding from Hainan Institute of Zhejiang University(0202-6602-A12201)the Distinguished Discipline Support Program of Zhejiang University(226-2024-00205,226-2022-00100).
文摘The Malvaceae family,the most diverse family in the order Malvales,consists of nine subfamilies.Within the Firmiana genus of the Sterculioideae subfamily,most species are considered globally vulnerable,yet their genomes remain unexplored.Here,we present a chromosome-level genome assembly for a representative Firmiana species,F.hainanensis,2n=40,totaling 1536 Mb.Phylogenomic analysis shows that F.hainanensis and Durio zibethinus have the closest evolutionary relationship,with an estimated divergence time of approximately 21 millions of years ago(MYA)and distinct polyploidization events in their histories.Evolutionary trajectory analyses indicate that fissions and fusions may play a crucial role in chromosome number variation(2n=14 to 2n=96).Analysis of repetitive elements among Malvaceae reveals that the Tekay subfamily(belonging to the Gypsy group)contributes to variation in genome size(ranging from 324 Mb to 1620 Mb).Additionally,genes associated with P450,peroxidase,and microtubules,and thereby related to cell wall biosynthesis,are significantly contracted in F.hainanensis,potentially leading to its lower wood density relative to Hopea hainanensis.Overall,our study provides insights into the evolution of chromosome number,genome size,and the genetic basis of cell wall biosynthesis in Malvaceae species.
基金This work was supported by the National Key Research and Development Program of China(2018YFD1000601 and 2019YFD1001601)the National Natural Science Foundation of China(31800180)+2 种基金the Natural Science Foundation of Anhui Province of China(1908085MC75)the China Postdoctoral Science Foundation(2017M621992)and the special funds for tea germplasm garden construction(2060502 and 201834040003).
文摘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.
基金supported by grants from the National Key R&D Program of China(2016YFD040024)the Agricultural Science and Technology Innovation Program of China(CAAS-ASTIP-lBFC)the National Natural Science Foundation of China(31772323,31871678,and 31972000).
文摘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.
基金the National Natural Science Foundation of China(90717009)the Chinese National Basic Research Program of the Ministry of Science and Technology of China(2010CB126000)
文摘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.
基金supported by the National Key R&D Program of China(Grant No.2017YFD0600703)the National Forestry Public Welfare Industry Research Project of China(Grant No.201204403)+2 种基金the Outstanding Youth Project of the Education Department of Hunan Province,China(Grant No.17B279)the US Department of AgricultureAgricultural Research Service(USDA-ARS)National Program for Quality and Utilization of Agricultural Products(NP 306Grant No.CRIS 6054-41000-103-00-D).
文摘Tung tree(Vernicia fordii)is an economically important woody oil plant that produces tung oil rich in eleostearic acid.Here,we report a high-quality chromosome-scale genome sequence of tung tree.The genome sequence was assembled by combining Illumina short reads,Pacific Biosciences single-molecule real-time long reads,and Hi-C sequencing data.The size of tung tree genome is 1.12 Gb,with 28,422 predicted genes and over 73%repeat sequences.The V.fordii underwent an ancient genome triplication event shared by core eudicots but no further wholegenome duplication in the subsequent ca.34.55 million years of evolutionary history of the tung tree lineage.Insertion time analysis revealed that repeat-driven genome expansion might have arisen as a result of long-standing long terminal repeat retrotransposon bursts and lack of efficient DNA deletion mechanisms.The genome harbors 88 resistance genes encoding nucleotide-binding sites;17 of these genes may be involved in early-infection stage of Fusarium wilt resistance.Further,651 oil-related genes were identified,88 of which are predicted to be directly involved in tung oil biosynthesis.Relatively few phosphoenolpyruvate carboxykinase genes,and synergistic effects between transcription factors and oil biosynthesis-related genes might contribute to the high oil content of tung seed.The tung tree genome constitutes a valuable resource for understanding genome evolution,as well as for molecular breeding and genetic improvements for oil production.
基金supported by the Key Research and Development Projects in Tibet:Preservation of Characteristic Biological Germplasm Resources and Utilization of Gene Technology in Tibet(XZ202001ZY0016N)National Natural Science Foundation of China(32072980)Special Finance of Tibet Autonomous Region(XZNKY-2019-C-053)。
文摘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.
基金This work was supported by the Ministry of Science and Technology,the National Key Research and Development Program of China(2021YFC2100800)the National Natural Science Foundation of China(31800719,31861143017,21621004).
文摘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.
基金supports from The Innovation and Application Engineering Technology Research Center of Ornamental Plant Germplasm Resources in Fujian Province (115-PTJH16005)The Plateau Discipline Construction Program of Fujian Province (115712018010)Special Fund for Forest Scientific Research in the Public Welfare (201204604)。
文摘Melastomataceae has abundant morphological diversity with high economic and ornamental merit in Myrtales. The phylogenetic position of Myrtales is still contested. Here, we report the chromosome-level genome assembly of Melastoma dodecandrum in Melastomataceae. The assembled genome size is299.81 Mb with a contig N50 value of 3.00 Mb. Genome evolution analysis indicated that M. dodecandrum,Eucalyptus grandis, and Punica granatum were clustered into a clade of Myrtales and formed a sister group with the ancestor of fabids and malvids. We found that M. dodecandrum experienced four whole-genome polyploidization events: the ancient event was shared with most eudicots, one event was shared with Myrtales, and the other two events were unique to M. dodecandrum. Moreover, we identified MADS-box genes and found that the AP1-like genes expanded, and AP3-like genes might have undergone subfunctionalization. The SUAR63-like genes and AG-like genes showed different expression patterns in stamens, which may be associated with heteranthery. In addition, we found that LAZY1-like genes were involved in the negative regulation of stem branching development, which may be related to its creeping features. Our study sheds new light on the evolution of Melastomataceae and Myrtales, which provides a comprehensive genetic resource for future research.
基金supported by the National Natural Science Foundation of China(No.42171063)Southeast Asia Biodiversity Research Institute,Chinese Academy of Sciences(No.Y4ZK111B01)+6 种基金the Special Fund for ScientificResearch of Shanghai Landscaping&City Appearance Administrative Bureau(G242414,G242416)the“Yunnan Revitalization Talent Support Program”in Yunnan Province(XDYC-QNRC-2022-0028)Yunnan Revitalization Talent Support Program“Innovation Team”Project(202405AS350019)the CAS“Light of West China”Programthe 14th Five-Year Plan of Xishuangbanna Tropical Botanical Garden,Chinese Academy Sciences(XTBG-1450303)the European Research Council(ERC)under the European Union's Horizon 2020 research and innovation program(No.833522)GhentUniversity(Methusalem funding,BOF.MET.2021.0005.01).
文摘Genetic information has been instrumental in elucidating the relationship between the East Asian Summer Monsoon(EASM)and subtropical evergreen broad-leaved forests(EBLFs).However,how the genomic insights of EBLFs’species correspond to environmental shifts induced by the EASM remains limited.In this study,we investigated the adaptive mechanisms of evergreen Engelhardia species in response to the EASM through genome sequencing and comparative genomic analyses from the de novo genome assemblies of fiveclosely related Engelhardia taxa and one Rhoiptelea species.Our findingsrevealed that the divergence of evergreen trees from their sister deciduous species is closely associated with the onset and intensification of the EASM.This genomic transitionmayhave coincided with a significantexpansion of the terpene synthase(TPS)gene family in E.fenzelii,driven by four distinct modes of gene duplication.This expansion enhances the biosynthesis of terpene volatiles,providing a defensive mechanism against potential herbivory in EASM affected environments.We also identifieda shared whole-genome duplication(WGD)event across Engelhardia,along with substantial differences in transposable element(TE)composition and activity,which contributed to genome size variation between E.fenzelii and E.roxburghiana.In addition,demographic analyses revealed a continuous population decline over the past 10 million years,further exacerbated by recenthumandisturbance,underscoring the conservation urgency for these species.These results not only provide preliminary insights into the complex evolutionary dynamics within the Engelhardia genus from genomic insights(e.g.,the intricate relationships between genomic variations,environmental changes,and adaptive responses driven by significantclimatic events such as the EASM),but also provides valuable insights into the conservation significance of EBLFs.
基金supported by the National Natural Science Foundation of China(32270217,31970205,31770211)Metasequoia funding of Nanjing Forestry University to YY。
文摘Amborella trichopoda(Amborellaceae;hereafter simply Amborella)(Fig.1A)is a shrub endemic to New Caledonia in the Southwest Pacific that represents the sole sister species of all other extant angiosperms(Qiu et al.,1999;One Thousand Plant Transcriptomes Initiative,2019).Due to its unique phylogenetic status,it holds tremendous interest for botanists.The nuclear and mitochondrial genomes of Amborella were first published in 2013,providing valuable resources for studies on genome and gene family evolution,phylogenomics,and flower development,despite the fact that the assembly is heavily fragmented(Amborella Genome Project,2013;Rice et al.,2013).In 2024,a haplotype-resolved Amborella genome assembly was published,showing significant improvement in quality and completeness(Carey et al.,2024).
基金Acknowledgements We sincerely thank Dr. Taihachi Kawahara, Dr. Yang Xinming for supplying the seeds. This work was supported by the National Natural Science Foundation of China （30170063）.
文摘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.
基金supported partially by the Australian Government through the Australian Research Council Centres of Excellence funding scheme(project CE200100029)。
文摘Background:Tandem gene repeats naturally occur as important genomic features and determine many traits in living organisms,like human diseases and microbial productivities of target bioproducts.Methods:Here,we developed a bacterial type-II toxin-antitoxin-mediated method to manipulate genomic integration of tandem gene repeats in Saccharomyces cerevisiae and further visualised the evolutionary trajectories of gene repeats.We designed a tri-vector system to introduce toxin-antitoxin-driven gene amplification modules.Results:This system delivered multi-copy gene integration in the form of tandem gene repeats spontaneously and independently from toxin-antitoxin-mediated selection.Inducing the toxin(RelE)expressing via a copper(II)-inducible CUP1 promoter successfully drove the in-situ gene amplification of the antitoxin(RelB)module,resulting in~40 copies of a green fluorescence reporter gene per copy of genome.Copy-number changes,copy-number increase and copy-number decrease,and stable maintenance were visualised using the green fluorescence protein and blue chromoprotein AeBlue as reporters.Copy-number increases happened spontaneously and independent on a selection pressure.Increased copy number was quickly enriched through toxin-antitoxin-mediated selection.Conclusion:In summary,the bacterial toxin-antitoxin systems provide a flexible mechanism to manipulate gene copy number in eukaryotic cells and can be exploited for synthetic biology and metabolic engineering applications.
基金supported in part by a grant from Northern Illinois University Foundation to Long MAONational Institutes of Health(NIH)grant to Mitrick JOHNS and Long MAO(No.44-G1A62164)a grant from the National Natural Science Foundation of China for oversea young scholars to Long MAO(No.30228022).
文摘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.
基金financially supported by the National Natural Science Foundation of China(Grant No.31772338)the Basic Scientific Research Business Special Project of Jiangsu Academy of Agricultural Sciences(Grant No.0090756100ZX)。
文摘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.
