Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorl...Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored.This study generated a diploid genome assembly for the golden pheasant(Chrysolophus pictus),a species distinguished by the vibrant plumage of males.Each haploid genome assembly included complete chromosomalmodels,incorporatingall microchromosomes.Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes(dot chromosomes),with an average copy number of 54.Structural variation between the haploid genomes was primarily shaped by large insertions and deletions(indels),with minimal contributions from inversions or duplications.Approximately 28%of these large indels were associated with recent insertions of transposable elements,despite their typically low activity in bird genomes.Evidence for significant effects of transposable elements on gene expression was minimal.Evolutionary strata on the sex chromosomes were identified,along with a drastic rearrangement of the W chromosome.These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.展开更多
The fine-tuned expression dynamics of the effector genes are pivotal for the transition from vegetative growth to host colonization of pathogenic filamentous fungi.However,mechanisms underlying the dynamic regulation ...The fine-tuned expression dynamics of the effector genes are pivotal for the transition from vegetative growth to host colonization of pathogenic filamentous fungi.However,mechanisms underlying the dynamic regulation of these genes remain largely unknown.Here,through comparative transcriptome and chromatin immunoprecipitation sequencing(ChIP-seq)analyses of the methyltransferase PoKmt6 in rice blast fungus Pyricularia oryzae(syn.Magnaporthe oryzae),we found that PoKmt6-mediated H3K27me3 deposition was enriched mainly at fast-evolving regions and contributed to the silencing of a subset of secreted proteins(SP)and transposable element(TE)families during the vegetative growth of P.oryzae.Intriguingly,we observed that a group of SP genes,which were depleted of H3K27me3 modification,could also be silenced via the H3K27me3-mediated repression of the nearby TEs.In conclusion,our results indicate that H3K27me3 modification mediated by PoKmt6 regulates the expression of some SP genes in fast-evolving regions through the suppression of nearby TEs.展开更多
Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories...Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.展开更多
Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unkn...Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.展开更多
Two miniature inverted-repeat transposable elements（MITEs）, MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus＇ known to be associated with citrus Huanglongbing（HLB, yellow shoo...Two miniature inverted-repeat transposable elements（MITEs）, MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus＇ known to be associated with citrus Huanglongbing（HLB, yellow shoot disease）. MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus＇ isolates from China, the United States and Brazil. Out of the 12 sequence types, three（T4, T5-2, T6） were reported for the first time. Recombination events were found in the two unique sequence types（T5-2 and T6） which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, S？o Paulo isolates and a few Florida isolates.展开更多
Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chr...Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.展开更多
Mutator transposable element （Mu） has been used as an effective tool to clone maize （Zea mays L.） genes. One opaque endosperm mutant （miol6） was identified in a pool of Mu inserted mutants. A modified method, te...Mutator transposable element （Mu） has been used as an effective tool to clone maize （Zea mays L.） genes. One opaque endosperm mutant （miol6） was identified in a pool of Mu inserted mutants. A modified method, termed the double selected amplification of insertion flanking fragments （DSAIFF）, was employed to isolate the Mu flanking fragments （MFFs） of miol6. The target site duplications （TSDs） isolated from the Msp I and Mse I digested MFFs had a same 9-bp sequence and were confirmed to be the flanking sequence of one identically inserted gene. Co-segregation analysis suggested that the MFFs were associated with the mutant opaque endosperm, and miol6 was mapped in silico onto the physical position ranged from 229 965 021 to 229 965 409 bp of the maize chromosome 4.09 bin. The full-length cDNA of the wild-type gene was obtained by an RT-PCR primer-scanning technique, and Mio16 was found to putatively encode a homolog of the Arabidopsis MAP3K delta-1 protein kinase. RT-PCR result the mRNA expression of miol6 region anchored by primers Mu20 and af276 was not interrupted by Mu insertion. Further researches will be done to elucidate how the expression of miol6 is alternated by Mu insertion.展开更多
Miniature inverted-repeat transposable elements(MITEs)are a group of DNA transposable element(TE)which preferentially distributed with gene associated regions.Tens of MITEs families have been revealed in Brassica napu...Miniature inverted-repeat transposable elements(MITEs)are a group of DNA transposable element(TE)which preferentially distributed with gene associated regions.Tens of MITEs families have been revealed in Brassica napus genome,they scatter across the genome with tens of thousands copies and produce polymorphisms both intra-and inter-species.Our previous studies revealed a Tourist-like MITE,Monkey King,associated with vernalization requirement of B.napus,however there are still few studies reveal MITE association with agricultural traits in B.napus.In the present study,80 polymorphic markers were developed from 55 MITEs,and used to evaluate genetic diversity in a panel of B.napus accessions consisting of 101 natural and 25 synthetic genotypes.Five agricultural traits,oil content,glucosinolate content,erucic acid content,weight of thousand seeds(WTS)and plant height,were investigated across 3-years field experiments,in addition,two traits,hypocotyl length and root length,were evaluated at the 4-leaf stage in the laboratory.Correlations between the MITE-based markers and seven traits were analyzed,finally,10 polymorphic markers produced by 6 pairs of MITE specific primers were revealed relatively high correlation with 5 traits.Two polymorphic markers were anchored with two candidate genes,BnaA02g13530D and BnaA08g20010D,respectively,which may contribute to glucosinolate content and WTS.This research may contribute to genetic improvement through utilization of MITE-induced polymorphisms in Brassica species.展开更多
Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fun...Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.展开更多
Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit...Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit plant growth and development,and reduce species richness comparing to tropical continental islands with mesophytic habitats(Li et al.,2024;Ren et al.,2017;Tu et al.,2022,2024).Coupled with global climate changes,these adverse conditions have been being exacerbated,leading to extensive degradation of ecosystems throughout the tropical coral islands(Li et al.,2021).Native insular plant resources provide enormous potentials in island greening and ecological restoration,since they have colonized and become well adapted to the specialized habitat on tropical coral islands,evolving a series of functional traits and molecular strategies to accommodate the abiotic stresses.Thus,understanding the genomic make-up of these plants will help uncover molecular mechanisms underlying adaptation to tropical coral islands.However,contrary to the numerous genomic studies done for other extreme habitats,such as deserts(Hu et al.,2021;Ma et al.,2013),alpine regions(Zhang et al.,2023),intertidal habitats(Feng et al.,2021;Hu et al.,2020;Natarajan et al.,2021),and karst caves(Feng et al.,2020),molecular adaptation of plants on the tropical coral islands remains to be elucidated.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
Transposable elements(TEs),once considered genomic"junk",are now recognized as critical regulators of genome function and human disease.These mobile genetic elements—including retrotransposons(long interspe...Transposable elements(TEs),once considered genomic"junk",are now recognized as critical regulators of genome function and human disease.These mobile genetic elements—including retrotransposons(long interspersed nuclear elements[LINE-1],Alu,short interspersed nuclear element-variable numbers of tandem repeats-Alu[SVA],and human endogenous retrovirus[HERV])and DNA transposons—are tightly regulated by multilayered mechanisms that operate from transcription through to genomic integration.Although typically silenced in somatic cells,TEs are transiently activated during key developmental stages—such as zygotic genome activation and cell fate determination—where they influence chromatin architecture,transcriptional networks,RNA processing,and innate immune responses.Dysregulation of TEs,however,can lead to genomic instability,chronic inflammation,and various pathologies,including cancer,neurodegeneration,and aging.Paradoxically,their reactivation also presents new opportunities for clinical applications,particularly as diagnostic biomarkers and therapeutic targets.Understanding the dual role of TEs—and balancing their contributions to normal development and disease—is essential for advancing novel therapies and precision medicine.展开更多
Polyploidization is a fundamental evolutionary process in plants,including bread wheat.In the present study,we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58(AK58),a...Polyploidization is a fundamental evolutionary process in plants,including bread wheat.In the present study,we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58(AK58),a modern elite polyploid wheat cultivar with a recently released reference genome,and in other wheat genomes,including landraces,synthetic wheat,and several breeding lines.Over 40% of transposable element(TE)families exhibit biased distribution across the three wheat subgenomes.Approximately 95.0%(113421)of genes are co-located with TEs,and these variable TEs significantly contribute to homoeologous divergence.We found that about 80%of triad homoeologs are divergent due to differences in expression or sub-functionalization.In addition,subgenome divergence potentially promote polyploid wheat domestication and improvement by increasing favorable homoeoallele combinations.Our findings suggest that homoeolog divergence contributes to the adaptation,domestication,and improvement of hexaploid wheat.The contribution of subgenomic divergence to polyploid heterosis is also discussed.This study provides a valuable resource for the investigation of how TEs drive homoeologous divergence during wheat domestication and improvement.展开更多
A twin ovary mutant derived from the doubled haploid (DH) progeny of a cross,02428/Gui 630, was presumably related to the transposition of some transposable elements. Up to date, all reported the active transposable ...A twin ovary mutant derived from the doubled haploid (DH) progeny of a cross,02428/Gui 630, was presumably related to the transposition of some transposable elements. Up to date, all reported the active transposable elements in rice (Oryza sativa L.) are copia like retrotransposons. In the present study, the reverse transcriptase domains of copia like retrotransposons were amplified from the total DNA isolated from the mutant plants with the degenerated oligonucleotide primers for the domain. Three cloned insert DNAs, R33 1, R33 4 and R33 8, representing putative different copia like retrotransposons were screened out. Two of them displayed high polymorphism between “Zhaiyeqing 8” and “Jingxi 17”. Nine of the polymorphic bands were mapped on seven rice chromosomes. Sequencing analysis revealed that stop codons frequently occur in the sequence of R33 8, while both R33 1 and R33 4 contain a continuous coding region for 81 putative amino acid residues. No significant variation in hybridization patterns was found between indica and japonica rice or among 26 varieties of indica rice when R33 1 was used as a probe. Nevertheless, when R33 4 was used as a probe, high polymorphisms were detected both between indica and japonica rice and among 26 indica varieties, implying that this element might still be active in rice genomes.展开更多
Marker free is a rapidly developed strategy that offers a new approach for the elimination of public concerns caused by the selectable marker genes conferring antibiotic or herbicide resistance and so on. Furthermore,...Marker free is a rapidly developed strategy that offers a new approach for the elimination of public concerns caused by the selectable marker genes conferring antibiotic or herbicide resistance and so on. Furthermore, marker_free transgenic plants (MFTPs) have a number of special advantages, such as decreasing the concerns about safety of selectable marker and stacking transgenes progressively into transgenic plants, which significantly owns potential application value. Major approaches developed recently for obtaining MFTPs were reviewed in this paper.展开更多
The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb fi...The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.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
基金supported by the Foundation of Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration in Longdong (LDSWZY202103)Natural Science Foundation of Gansu Province (22JR5RM210)to B.P.L.Gansu Ziwuling Ecosystem Observation and Research Station (20JR10RA658)。
文摘Avian genomes exhibit compact organization and remarkable chromosomal stability.However,the extent and mechanisms by which structural variation in avian genomes differ from those in other vertebrate lineages are poorly explored.This study generated a diploid genome assembly for the golden pheasant(Chrysolophus pictus),a species distinguished by the vibrant plumage of males.Each haploid genome assembly included complete chromosomalmodels,incorporatingall microchromosomes.Analysis revealed extensive tandem amplification of immune-related genes across the smallest microchromosomes(dot chromosomes),with an average copy number of 54.Structural variation between the haploid genomes was primarily shaped by large insertions and deletions(indels),with minimal contributions from inversions or duplications.Approximately 28%of these large indels were associated with recent insertions of transposable elements,despite their typically low activity in bird genomes.Evidence for significant effects of transposable elements on gene expression was minimal.Evolutionary strata on the sex chromosomes were identified,along with a drastic rearrangement of the W chromosome.These analyses of the high-quality diploid genome of the golden pheasant provide valuable insights into the evolutionary patterns of structural variation in avian genomes.
基金the grants from the National Natural Science Foundation of China(U1805232,31770156,and 32172365)the China Postdoctoral Science Foundation(2021M690637)。
文摘The fine-tuned expression dynamics of the effector genes are pivotal for the transition from vegetative growth to host colonization of pathogenic filamentous fungi.However,mechanisms underlying the dynamic regulation of these genes remain largely unknown.Here,through comparative transcriptome and chromatin immunoprecipitation sequencing(ChIP-seq)analyses of the methyltransferase PoKmt6 in rice blast fungus Pyricularia oryzae(syn.Magnaporthe oryzae),we found that PoKmt6-mediated H3K27me3 deposition was enriched mainly at fast-evolving regions and contributed to the silencing of a subset of secreted proteins(SP)and transposable element(TE)families during the vegetative growth of P.oryzae.Intriguingly,we observed that a group of SP genes,which were depleted of H3K27me3 modification,could also be silenced via the H3K27me3-mediated repression of the nearby TEs.In conclusion,our results indicate that H3K27me3 modification mediated by PoKmt6 regulates the expression of some SP genes in fast-evolving regions through the suppression of nearby TEs.
基金This study was supported by the National Natural Science Foundation of China(31671319,31722050,32061130208)Natural Science Foundation of Zhejiang Province(LD19C190001)+5 种基金European Research Council Starting Grant(grant agreement 677696)to Q.Z.the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB31020000,XDB13000000)International Partnership Program of Chinese Academy of Sciences(152453KYSB20170002)Carlsberg Foundation(CF16-0663)Villum Foundation(25900)to G.J.ZWe thank China National Genebank at BGI for contributing to the sequencing.We would like to thank Christopher C.Witt,Mariel L.Campbell and Ariel M.Gaffney from the Museum of Southwestern Biology,Gary Graves from Smithsonian Institute,Robb T.Brumfield and Donna L.Dittman from Louisiana State University Museum of Natural Science,Jack Withrow and Andy Kratter from Florida Museum of Natural History,University of New Mexico for providing bird DNA samples for this work.
文摘Palaeognathae includes ratite and tinamou species that are important for understanding early avian evolution.Here,we analyzed the whole-genome sequences of 15 paleognathous species to infer their demographic histories,which are presently unknown.We found that most species showed a reduction of population size since the beginning of the last glacial period,except for those species distributed in Australasia and in the far south of South America.Different degrees of contraction and expansion of transposable elements(TE)have shaped the paleognathous genome architecture,with a higher transposon removal rate in tinamous than in ratites.One repeat family,AviRTE,likely underwent horizontal transfer from tropical parasites to the ancestor of little and undulated tinamous about 30 million years ago.Our analysis of gene families identified rapid turnover of immune and reproductionrelated genes but found no evidence of gene family changes underlying the convergent evolution of flightlessness among ratites.We also found that mitochondrial genes have experienced a faster evolutionary rate in tinamous than in ratites,with the former also showing more degenerated W chromosomes.This result can be explained by the Hill-Robertson interference affecting genetically linked W chromosomes and mitochondria.Overall,we reconstructed the evolutionary history of the Palaeognathae populations,genes,and TEs.Our findings of co-evolution between mitochondria and W chromosomes highlight the key difference in genome evolution between species with ZW sex chromosomes and those with XY sex chromosomes.
基金supported by the National Natural Science Foundation of China(32160781)。
文摘Regulatory sequences and transposable elements(TEs)account for a large proportion of the genomic sequences of species;however,their roles in gene transcription,especially tissue-specific expression,remain largely unknown.Pigs serve as an excellent animal model for studying genomic sequence biology due to the extensive diversity among their wild and domesticated populations.Here,we conducted an integrated analysis using H3K27ac ChIP-seq,H3K4me3 ChIP-seq,and RNA-seq data from 10 different tissues of seven fetuses and eight closely related adult pigs.We aimed to annotate the regulatory elements and TEs to elucidate their associations with histone modifications and mRNA expression across different tissues and developmental stages.Based on correlation analysis between mRNA expression and H3K27ac and H3K4me3 peak activity,results indicated that H3K27ac exhibited stronger associations with gene expression than H3K4me3.Furthermore,1.45%of TEs overlapped with either the H3K27ac or H3K4me3 peaks,with the majority displaying tissue-specific activity.Notably,a TE subfamily(LTR4C_SS),containing binding motifs for SIX1 and SIX4,showed specific enrichment in the H3K27ac peaks of the adult and fetal ovaries.RNA-seq analysis also revealed widespread expression of TEs in the exons or promoters of genes,including 4688 TE-containing transcripts with distinct development stage-specific and tissue-specific expression.Of note,1967 TE-containing transcripts were enriched in the testes.We identified a long terminal repeat(LTR),MLT1F1,acting as a testis-specific alternative promoter in SRPK2(a cell cycle-related protein kinase)in our pig dataset.This element was also conserved in humans and mice,suggesting either an ancient integration of TEs in genes specifically expressed in the testes or parallel evolutionary patterns.Collectively,our findings demonstrate that TEs are deeply embedded in the genome and exhibit important tissue-specific biological functions,particularly in the reproductive organs.
基金provided by the Special Fund for Agro-Scientific Research in the Public Interest, China (201003067-02)the Natural Science Foundation Project of CQ CSTC (cstc2012jj A80025)the Fundamental Research Funds for the Central Universities, China (XDJK2014A001, XDJK2014D004)
文摘Two miniature inverted-repeat transposable elements（MITEs）, MCLas-A and MCLas-B, were recently identified from ‘Candidatus Liberibacter asiaticus＇ known to be associated with citrus Huanglongbing（HLB, yellow shoot disease）. MCLas-A was suggested as an active MITE because of its mobility. The immediate upstream gene of the two MITEs was predicted to be a putative transposase. The goal of this study is to analyze the sequence variation in the upstream putative transposase of MITEs and explore the possible correlation between sequence variation of transposase gene and MITE activity. PCR and sequence analysis showed that 12 sequence types were found in six major amplicon types from 43 representative ‘Ca. L. asiaticus＇ isolates from China, the United States and Brazil. Out of the 12 sequence types, three（T4, T5-2, T6） were reported for the first time. Recombination events were found in the two unique sequence types（T5-2 and T6） which were detected in all Brazilian isolates. Notably, no sequence variation or recombination events were detected in the upstream putative transposase gene of MCLas-A, suggesting the conservation of the transposase gene might be closely related with the MITE activity. Phylogenetic analysis demonstrated two well supported clades including five subclades were identified, clearly reflecting the geographical origins of isolates, especially that of Ruili isolates, S？o Paulo isolates and a few Florida isolates.
基金supported by National Key Research and Development Program of China(2021YFF1000601).
文摘Background:A comprehensive landscape of chromatin states for multiple mammalian tissues is essential for elucidating the molecular mechanism underlying regulatory variants on complex traits.However,the genome-wide chromatin accessibility has been only reported in limited tissue types in pigs.Results:Here we report a genome-wide landscape of chromatin accessibility of 20 tissues in two female pigs at ages of 6 months using ATAC-seq,and identified 557,273 merged peaks,which greatly expanded the pig regulatory ele-ment repository.We revealed tissue-specific regulatory elements which were associated with tissue-relevant biologi-cal functions.We identified both positive and negative significant correlations between the regulatory elements and gene transcripts,which showed distinct distributions in terms of their strength and distances from corresponding genes.We investigated the presence of transposable elements(TEs)in open chromatin regions across all tissues,these included identifications of porcine endogenous retroviruses(PERVs)exhibiting high accessibility in liver and homology of porcine specific virus sequences to universally accessible transposable elements.Furthermore,we prior-itized a potential causal variant for polyunsaturated fatty acid in the muscle.Conclusions:Our data provides a novel multi-tissues accessible chromatin landscape that serve as an important resource for interpreting regulatory sequences in tissue-specific and conserved biological functions,as well as regula-tory variants of loci associated with complex traits in pigs.
基金supported by the High-Tech R&D Program of China(2006AA10A106)the open funds of the National Key Laboratory of Crop Genetic Improvement and China National Fundamental Fund of Personnel Training (J0730649)
文摘Mutator transposable element （Mu） has been used as an effective tool to clone maize （Zea mays L.） genes. One opaque endosperm mutant （miol6） was identified in a pool of Mu inserted mutants. A modified method, termed the double selected amplification of insertion flanking fragments （DSAIFF）, was employed to isolate the Mu flanking fragments （MFFs） of miol6. The target site duplications （TSDs） isolated from the Msp I and Mse I digested MFFs had a same 9-bp sequence and were confirmed to be the flanking sequence of one identically inserted gene. Co-segregation analysis suggested that the MFFs were associated with the mutant opaque endosperm, and miol6 was mapped in silico onto the physical position ranged from 229 965 021 to 229 965 409 bp of the maize chromosome 4.09 bin. The full-length cDNA of the wild-type gene was obtained by an RT-PCR primer-scanning technique, and Mio16 was found to putatively encode a homolog of the Arabidopsis MAP3K delta-1 protein kinase. RT-PCR result the mRNA expression of miol6 region anchored by primers Mu20 and af276 was not interrupted by Mu insertion. Further researches will be done to elucidate how the expression of miol6 is alternated by Mu insertion.
基金supported by National Natural Science Foundation of China(No.31501341)Outstanding Youth Foundation of Henan Academy of Agricultural Sciences(No.2016YQ29).
文摘Miniature inverted-repeat transposable elements(MITEs)are a group of DNA transposable element(TE)which preferentially distributed with gene associated regions.Tens of MITEs families have been revealed in Brassica napus genome,they scatter across the genome with tens of thousands copies and produce polymorphisms both intra-and inter-species.Our previous studies revealed a Tourist-like MITE,Monkey King,associated with vernalization requirement of B.napus,however there are still few studies reveal MITE association with agricultural traits in B.napus.In the present study,80 polymorphic markers were developed from 55 MITEs,and used to evaluate genetic diversity in a panel of B.napus accessions consisting of 101 natural and 25 synthetic genotypes.Five agricultural traits,oil content,glucosinolate content,erucic acid content,weight of thousand seeds(WTS)and plant height,were investigated across 3-years field experiments,in addition,two traits,hypocotyl length and root length,were evaluated at the 4-leaf stage in the laboratory.Correlations between the MITE-based markers and seven traits were analyzed,finally,10 polymorphic markers produced by 6 pairs of MITE specific primers were revealed relatively high correlation with 5 traits.Two polymorphic markers were anchored with two candidate genes,BnaA02g13530D and BnaA08g20010D,respectively,which may contribute to glucosinolate content and WTS.This research may contribute to genetic improvement through utilization of MITE-induced polymorphisms in Brassica species.
基金supported by the National Science Foundation(NSF),Award Number 1557995(IS,AZZ)IS was partially supported by the U.S.Department of Agriculture's National Institute of Food and Agriculture(USDA-NIFA)Hatch project CA-D-PPA-2739-H.
文摘Fungi are a diverse kingdom characterized by remarkable genomic plasticity that facilitates pathogenicity and adaptation to adverse environmental conditions.In this review,we delve into the dynamic organization of fungal genomes and its implications for host adaptation and antifungal resistance.We examine key features and the heterogeneity of genomes across different fungal species,including but not limited to their chromosome content,DNA composition,distribution and arrangement of their content across chromosomes,and other major traits.We further highlight how this variability in genomic traits influences their virulence and adaptation to adverse conditions.Fungal genomes exhibit large variations in size,gene content,and structural features,such as the abundance of transposable elements(TEs),compartmentalization into gene-rich and TE-rich regions,and the presence or absence of dispensable chromosomes.Genomic structural variations are equally diverse in fungi,ranging from whole-chromosome duplications that may enhance tolerance to antifungal compounds,to targeted deletion of effector encoding genes that may promote virulence.Finally,the often-overlooked fungal mitochondrial genomes can also affect virulence and resistance to fungicides.Such and other features of fungal genome organization are reviewed and discussed in the context of host-microbe interactions and antifungal resistance.
基金supported by the National Natural Science Foundation of China(32170232,32070222,32271613)the National Key R&D Programof China(Key Special Project for Marine Environmental Security and Sustainable Development of Coral Reefs 2021-400)+1 种基金Guangdong Science and Technology Program(2024B1212050007)the National Key Research and Development Program of China(2021YFC3100405)。
文摘Tropical coral islands represent one of the extremely stressful ecosystems,characterized by high salinity,seasonal drought,heat,strong ultraviolet radiation,and infertile soil,which constraint species occurrence,limit plant growth and development,and reduce species richness comparing to tropical continental islands with mesophytic habitats(Li et al.,2024;Ren et al.,2017;Tu et al.,2022,2024).Coupled with global climate changes,these adverse conditions have been being exacerbated,leading to extensive degradation of ecosystems throughout the tropical coral islands(Li et al.,2021).Native insular plant resources provide enormous potentials in island greening and ecological restoration,since they have colonized and become well adapted to the specialized habitat on tropical coral islands,evolving a series of functional traits and molecular strategies to accommodate the abiotic stresses.Thus,understanding the genomic make-up of these plants will help uncover molecular mechanisms underlying adaptation to tropical coral islands.However,contrary to the numerous genomic studies done for other extreme habitats,such as deserts(Hu et al.,2021;Ma et al.,2013),alpine regions(Zhang et al.,2023),intertidal habitats(Feng et al.,2021;Hu et al.,2020;Natarajan et al.,2021),and karst caves(Feng et al.,2020),molecular adaptation of plants on the tropical coral islands remains to be elucidated.
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supported by grants from Beijing Natural Science Foundation(No.JQ24033)the National Key Research and Development Program(No.2022YFA1302700)+1 种基金the National Natural Science Foundation of China(Nos.32350011,32270593,32070631,and 32400441)the China Postdoctoral Science Foundation(No.2024T170499).
文摘Transposable elements(TEs),once considered genomic"junk",are now recognized as critical regulators of genome function and human disease.These mobile genetic elements—including retrotransposons(long interspersed nuclear elements[LINE-1],Alu,short interspersed nuclear element-variable numbers of tandem repeats-Alu[SVA],and human endogenous retrovirus[HERV])and DNA transposons—are tightly regulated by multilayered mechanisms that operate from transcription through to genomic integration.Although typically silenced in somatic cells,TEs are transiently activated during key developmental stages—such as zygotic genome activation and cell fate determination—where they influence chromatin architecture,transcriptional networks,RNA processing,and innate immune responses.Dysregulation of TEs,however,can lead to genomic instability,chronic inflammation,and various pathologies,including cancer,neurodegeneration,and aging.Paradoxically,their reactivation also presents new opportunities for clinical applications,particularly as diagnostic biomarkers and therapeutic targets.Understanding the dual role of TEs—and balancing their contributions to normal development and disease—is essential for advancing novel therapies and precision medicine.
基金supported by the National Natural Science Foundation of China(91940301,32441002,32370341,and 32201844)the Natural Science Basic Research Plan in Shaanxi Province of China(2022JQ-172)+2 种基金Zhongyuan Scholar Program(234000510002)the National Key Research and Development Program of China(2021YFD1200601-04)the Hundred-Talent Program of Zhejiang University.
文摘Polyploidization is a fundamental evolutionary process in plants,including bread wheat.In the present study,we performed a comprehensive genome-wide analysis of dynamic homoeologous gene divergence in Aikang58(AK58),a modern elite polyploid wheat cultivar with a recently released reference genome,and in other wheat genomes,including landraces,synthetic wheat,and several breeding lines.Over 40% of transposable element(TE)families exhibit biased distribution across the three wheat subgenomes.Approximately 95.0%(113421)of genes are co-located with TEs,and these variable TEs significantly contribute to homoeologous divergence.We found that about 80%of triad homoeologs are divergent due to differences in expression or sub-functionalization.In addition,subgenome divergence potentially promote polyploid wheat domestication and improvement by increasing favorable homoeoallele combinations.Our findings suggest that homoeolog divergence contributes to the adaptation,domestication,and improvement of hexaploid wheat.The contribution of subgenomic divergence to polyploid heterosis is also discussed.This study provides a valuable resource for the investigation of how TEs drive homoeologous divergence during wheat domestication and improvement.
文摘A twin ovary mutant derived from the doubled haploid (DH) progeny of a cross,02428/Gui 630, was presumably related to the transposition of some transposable elements. Up to date, all reported the active transposable elements in rice (Oryza sativa L.) are copia like retrotransposons. In the present study, the reverse transcriptase domains of copia like retrotransposons were amplified from the total DNA isolated from the mutant plants with the degenerated oligonucleotide primers for the domain. Three cloned insert DNAs, R33 1, R33 4 and R33 8, representing putative different copia like retrotransposons were screened out. Two of them displayed high polymorphism between “Zhaiyeqing 8” and “Jingxi 17”. Nine of the polymorphic bands were mapped on seven rice chromosomes. Sequencing analysis revealed that stop codons frequently occur in the sequence of R33 8, while both R33 1 and R33 4 contain a continuous coding region for 81 putative amino acid residues. No significant variation in hybridization patterns was found between indica and japonica rice or among 26 varieties of indica rice when R33 1 was used as a probe. Nevertheless, when R33 4 was used as a probe, high polymorphisms were detected both between indica and japonica rice and among 26 indica varieties, implying that this element might still be active in rice genomes.
文摘Marker free is a rapidly developed strategy that offers a new approach for the elimination of public concerns caused by the selectable marker genes conferring antibiotic or herbicide resistance and so on. Furthermore, marker_free transgenic plants (MFTPs) have a number of special advantages, such as decreasing the concerns about safety of selectable marker and stacking transgenes progressively into transgenic plants, which significantly owns potential application value. Major approaches developed recently for obtaining MFTPs were reviewed in this paper.
基金This study was supported by the National Natural Science Foundation of China(NSFC,nos.31770331 and 31970318)Guangdong Basic and Applied Basic Research Foundation(no.2020B1515120023).
文摘The ultimate goal of genome assembly is a high-accuracy gapless genome.Here,we report a new assembly pipeline that is used to produce a gapless genome for the indica rice cultivar Minghui 63.The resulting 397.71-Mb final assembly is composed of 12 contigs with a contig N50 size of 31.93 Mb.Each chromosome is represented by a single contig and the genomic sequences of all chromosomes are gapless.Quality evaluation of this gapless genome assembly showed that gene regions in our assembly have the highest completeness compared with the other 15 reported high-quality rice genomes.Further comparison with the japonica rice genome revealed that the gapless indica genome assembly contains more transposable elements(TEs)and segmental duplications(SDs),the latter of which produce many duplicated genes that can affect agronomic traits through dose effect or sub-/neo-functionalization.The insertion of TEs can also affect the expression of duplicated genes,which may drive the evolution of these genes.Furthermore,we found the expansion of nucleotide-binding site with leucine-rich repeat disease-resistance genes and cis-zeatin-O-glucosyltransferase growth-related genes in SDs in the gapless indica genome assembly,suggesting that SDs contribute to the adaptive evolution of rice disease resistance and developmental processes.Collectively,our findings suggest that active TEs and SDs synergistically contribute to rice genome evolution.
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.
