Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play ...Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play a critical role in the stabilization and establishment of nascent plant polyploids as new species. To further study this issue, five wheat chromosome 7B_specific sequences, isolated from common wheat (Triticum aestivum L.) by chromosome microdissection, were characterized. The sequences were studied by genomic Southern hybridizations on a collection of polyploid wheats and their diploid progenitors. Four sequences hybridized to all polyploid species, but at the diploid level to only species closely related to the B_genome of polyploid wheat. This indicates that these sequences originated with the divergence of the diploid species, and was then vertically transmitted to polyploids. One sequence hybridized to all species at both the diploid and polyploid levels, suggesting its elimination after the polyploid wheat formation. The hybridization of this sequence to two synthetic polyploid wheats indicated that sequence elimination is a rapid event and probably related to methylation status of the sequence. Based on the above results, we suggest that selective changes of low_copy sequences occur rapidly after polyploid formation, which may contribute to the differentiation of chromosomes in newly formed allopolyploid wheats.展开更多
Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improveme...Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.展开更多
Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and transcription.However,the role of non-B-form DNA in centromeres,especially in polyploid wheat...Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and transcription.However,the role of non-B-form DNA in centromeres,especially in polyploid wheat,remains elusive.Here,we systematically analyzed seven non-B-form DNA motif profiles(A-phased DNA repeat,direct repeat,G-quadruplex,inverted repeat,mirror repeat,short tandem repeat,and Z-DNA)in hexaploid wheat.We found that three of these non-B-form DNA motifs were enriched at centromeric regions,especially at the CENH3-binding sites,suggesting that non-B-form DNA may create a favorable loading environment for the CENH3 nucleosome.To investigate the dynamics of centromeric non-B form DNA during the alloploidization process,we analyzed DNA secondary structure using CENH3 ChIP-seq data from newly formed allotetraploid wheat and its two diploid ancestors.We found that newly formed allotetraploid wheat formed more non-B-form DNA in centromeric regions compared with their parents,suggesting that non-B-form DNA is related to the localization of the centromeric regions in newly formed wheat.Furthermore,non-B-form DNA enriched in the centromeric regions was found to preferentially form on young LTR retrotransposons,explaining CENH3's tendency to bind to younger LTR.Collectively,our study describes the landscape of non-B-form DNA in the wheat genome,and sheds light on its potential role in the evolution of polyploid centromeres.展开更多
Common wheat(Triticum aestivum,BBAADD)is a major staple food crop worldwide.The diploid progenitors of the A and D subgenomes have been unequivocally identified;that of B,however,remains ambiguous and controversial bu...Common wheat(Triticum aestivum,BBAADD)is a major staple food crop worldwide.The diploid progenitors of the A and D subgenomes have been unequivocally identified;that of B,however,remains ambiguous and controversial but is suspected to be related to species of Aegilops,section Sitopsis.Here,we report the assembly of chromosome-level genome sequences of all five Sitopsis species,namely Aegilops bicornis,Ae.longissima,Ae.searsii,Ae.sharonensis,and Ae.speltoides,as well as the partial assembly of the Amblyopyrum muticum(synonym Aegilops mutica)genome for phylogenetic analysis.Our results reveal that the donor of the common wheat B subgenome is a distinct,and most probably extinct,diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae.speltoides and Am.muticum belong.In addition,we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex.The five Sitopsis species have various assembled genome sizes(4.11-5.89 Gb)with high proportions of repetitive sequences(85.99%-89.81%);nonetheless,they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex.Differences in genome size were primarily due to independent post-speciation amplification of transposons.We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding.These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex,as well as for wheat improvement.展开更多
Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks fo...Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named WheatCENet.WheatCENet is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered therein.Functional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.展开更多
Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respe...Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respectively.Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome.However,whether Ae.speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae.speltoides and the B subgenome remain unclear.Here,we assembled a high-quality reference genome for Ae.speltoides,resequenced 53 accessions from seven species(Aegilops bicornis,Aegilops longissima,Aegilops searsii,Aegilops sharonensis,Ae.speltoides,Aegilops mutica[syn.Amblyopyrum muticum],and Triticumdicoccoides)and revealed their genomic contributions to the wheat B subgenome.Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae.speltoides and the B subgenome.We classified five groups of conserved and non-conserved genes between Aegilops and Triticum,revealing their biological characteristics,differentiation in gene expression patterns,and collinear relationships between Ae.speltoides and the wheat B subgenome.We also identified gene families that expanded in Ae.speltoides during its evolution and 789 genes specific to Ae.speltoides.These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress.The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.展开更多
文摘Recent work revealed that, in the genomes of polyploid wheat, there exists a class of low_copy and chromosome_specific sequences that are labile upon polyploid formation. This class of sequences was proposed to play a critical role in the stabilization and establishment of nascent plant polyploids as new species. To further study this issue, five wheat chromosome 7B_specific sequences, isolated from common wheat (Triticum aestivum L.) by chromosome microdissection, were characterized. The sequences were studied by genomic Southern hybridizations on a collection of polyploid wheats and their diploid progenitors. Four sequences hybridized to all polyploid species, but at the diploid level to only species closely related to the B_genome of polyploid wheat. This indicates that these sequences originated with the divergence of the diploid species, and was then vertically transmitted to polyploids. One sequence hybridized to all species at both the diploid and polyploid levels, suggesting its elimination after the polyploid wheat formation. The hybridization of this sequence to two synthetic polyploid wheats indicated that sequence elimination is a rapid event and probably related to methylation status of the sequence. Based on the above results, we suggest that selective changes of low_copy sequences occur rapidly after polyploid formation, which may contribute to the differentiation of chromosomes in newly formed allopolyploid wheats.
基金supported by the National Natural Science Foundation of China (32322059 and 32272124)China Postdoctoral Science Foundation (2023M733807)+2 种基金Frontiers Science Center for Molecular Design Breeding (2022TC152)Pinduoduo-China Agricultural University Research Fund (PC2023B01016)the 2115 Talent Development Program of China Agricultural University.
文摘Bread wheat(Triticum aestivum)is an important crop and serves as a significant source of protein and calories for humans,worldwide.Nevertheless,its large and allopolyploid genome poses constraints on genetic improvement.The complex reticulate evolutionary history and the intricacy of genomic resources make the deciphering of the functional genome considerably more challenging.Recently,we have developed a comprehensive list of versatile computational tools with the integration of statistical models for dissecting the polyploid wheat genome.Here,we summarize the methodological innovations and applications of these tools and databases.A series of step-by-step examples illustrates how these tools can be utilized for dissecting wheat germplasm resources and unveiling functional genes associated with important agronomic traits.Furthermore,we outline future perspectives on new advanced tools and databases,taking into consideration the unique features of bread wheat,to accelerate genomic-assisted wheat breeding.
基金supported by the National Natural Science Foundation of China(31991212)the National Key Research and Development Program of China(2022YFF1003303)。
文摘Non-B-form DNA differs from the classic B-DNA double helix structure and plays a crucial regulatory role in replication and transcription.However,the role of non-B-form DNA in centromeres,especially in polyploid wheat,remains elusive.Here,we systematically analyzed seven non-B-form DNA motif profiles(A-phased DNA repeat,direct repeat,G-quadruplex,inverted repeat,mirror repeat,short tandem repeat,and Z-DNA)in hexaploid wheat.We found that three of these non-B-form DNA motifs were enriched at centromeric regions,especially at the CENH3-binding sites,suggesting that non-B-form DNA may create a favorable loading environment for the CENH3 nucleosome.To investigate the dynamics of centromeric non-B form DNA during the alloploidization process,we analyzed DNA secondary structure using CENH3 ChIP-seq data from newly formed allotetraploid wheat and its two diploid ancestors.We found that newly formed allotetraploid wheat formed more non-B-form DNA in centromeric regions compared with their parents,suggesting that non-B-form DNA is related to the localization of the centromeric regions in newly formed wheat.Furthermore,non-B-form DNA enriched in the centromeric regions was found to preferentially form on young LTR retrotransposons,explaining CENH3's tendency to bind to younger LTR.Collectively,our study describes the landscape of non-B-form DNA in the wheat genome,and sheds light on its potential role in the evolution of polyploid centromeres.
基金This study was supported by the Natural Science Foundation of China(31991211 to B.L.and 31970235 to L.F.L.)the Shanghai Pujiang Program(19PJ1401500 to L.F.L.),Israel Science Foundation(ISF)-China National Natural Science Foundation(NSFC)collaborative grants to B.L.(32061143001)and A.A.L.(3394/20)a China Postdoctoral Science Foundation grant(2021M690683).
文摘Common wheat(Triticum aestivum,BBAADD)is a major staple food crop worldwide.The diploid progenitors of the A and D subgenomes have been unequivocally identified;that of B,however,remains ambiguous and controversial but is suspected to be related to species of Aegilops,section Sitopsis.Here,we report the assembly of chromosome-level genome sequences of all five Sitopsis species,namely Aegilops bicornis,Ae.longissima,Ae.searsii,Ae.sharonensis,and Ae.speltoides,as well as the partial assembly of the Amblyopyrum muticum(synonym Aegilops mutica)genome for phylogenetic analysis.Our results reveal that the donor of the common wheat B subgenome is a distinct,and most probably extinct,diploid species that diverged from an ancestral progenitor of the B lineage to which the still extant Ae.speltoides and Am.muticum belong.In addition,we identified interspecific genetic introgressions throughout the evolution of the Triticum/Aegilops species complex.The five Sitopsis species have various assembled genome sizes(4.11-5.89 Gb)with high proportions of repetitive sequences(85.99%-89.81%);nonetheless,they retain high collinearity with other genomes or subgenomes of species in the Triticum/Aegilops complex.Differences in genome size were primarily due to independent post-speciation amplification of transposons.We also identified a set of Sitopsis genes pertinent to important agronomic traits that can be harnessed for wheat breeding.These newly assembled genome resources provide a new roadmap for evolutionary and genetic studies of the Triticum/Aegilops complex,as well as for wheat improvement.
基金supported by grants from the National Natural Science Foundation of China(Grant Nos.31970629 and 31771467 to ZS,and 31870209 to YJ).
文摘Genetic and epigenetic changes after polyploidization events could result in variable gene expression and modified regulatory networks.Here,using large-scale transcriptome data,we constructed co-expression networks for diploid,tetraploid,and hexaploid wheat species,and built a platform for comparing co-expression networks of allohexaploid wheat and its progenitors,named WheatCENet.WheatCENet is a platform for searching and comparing specific functional coexpression networks,as well as identifying the related functions of the genes clustered therein.Functional annotations like pathways,gene families,protein-protein interactions,microRNAs(miRNAs),and several lines of epigenome data are integrated into this platform,and Gene Ontology(GO)annotation,gene set enrichment analysis(GSEA),motif identification,and other useful tools are also included.Using WheatCENet,we found that the network of WHEAT ABERRANT PANICLE ORGANIZATION I(WAPOI)has more co-expressed genes related to spike development in hexaploid wheat than its progenitors.We also found a novel motif of CCWWWWWWGG(CArG)specifically in the promoter region of WAPO-Al,suggesting that neofunctionalization of the WAPO-AI gene affects spikelet development in hexaploid wheat.WheatCENet is useful for investigating co-expression networks and conducting other analyses,and thus facilitates comparative and functional genomic studies in wheat.
基金supported by the National Natural Science Foundation of China(grant no.31991213)the Talent Program and Agricultural Science and the Technology Innovation Program of CAAS,the China Postdoctoral Science Foundation(grant no.2022M713430)the Central Public-interest Scientific Institution Basal Research Fund(grant no.S2022ZD02).
文摘Wheat(Triticum aestivum,BBAADD)is an allohexaploid species that originated from two polyploidization events.The progenitors of the A and D subgenomes have been identified as Triticum urartu and Aegilops tauschii,respectively.Current research suggests that Aegilops speltoides is the closest but not the direct ancestor of the B subgenome.However,whether Ae.speltoides has contributed genomically to the wheat B subgenome and which chromosome regions are conserved between Ae.speltoides and the B subgenome remain unclear.Here,we assembled a high-quality reference genome for Ae.speltoides,resequenced 53 accessions from seven species(Aegilops bicornis,Aegilops longissima,Aegilops searsii,Aegilops sharonensis,Ae.speltoides,Aegilops mutica[syn.Amblyopyrum muticum],and Triticumdicoccoides)and revealed their genomic contributions to the wheat B subgenome.Our results showed that centromeric regions were particularly conserved between Aegilops and Triticum and revealed 0.17 Gb of conserved blocks between Ae.speltoides and the B subgenome.We classified five groups of conserved and non-conserved genes between Aegilops and Triticum,revealing their biological characteristics,differentiation in gene expression patterns,and collinear relationships between Ae.speltoides and the wheat B subgenome.We also identified gene families that expanded in Ae.speltoides during its evolution and 789 genes specific to Ae.speltoides.These genes can serve as genetic resources for improvement of adaptability to biotic and abiotic stress.The newly constructed reference genome and large-scale resequencing data for Sitopsis species will provide a valuable genomic resource for wheat genetic improvement and genomic studies.
