The Triticum-Aegilops complex groups demonstrated high cross-affinity with each other to overcome the barriers of distant hybridization(Loureiro et al.,2023).Distant hybridization involves two distinct yet closely rel...The Triticum-Aegilops complex groups demonstrated high cross-affinity with each other to overcome the barriers of distant hybridization(Loureiro et al.,2023).Distant hybridization involves two distinct yet closely related events:hybridization and genome doubling.Previous studies have indicated that bursts of transposable elements(TEs)can occur as a consequence or concomitant to hybridization or genome duplication(Parisod et al.,2010).This raises an important scientific question regarding how the TEs-rich centromere region copes with genomic shock(McClintock,1984).The Triticum-Aegilops species complexes,particularly in the F1,So,and subsequent early generations resulting from successive selfcrossing,offer an opportunity to investigate whether the centromere environment undergoes reconstruction and the associated mechanisms that maintain genomic stability.展开更多
Dear Editor,Legumes,including soybean and alfalfa,are vital agricultural crops worldwide,providing high-quality protein and oil sources for humans and animals.In addition,legumes also provide nitrogen for soil improve...Dear Editor,Legumes,including soybean and alfalfa,are vital agricultural crops worldwide,providing high-quality protein and oil sources for humans and animals.In addition,legumes also provide nitrogen for soil improvement,benefiting from their symbiotic associations with nitrogen-fixing bacteria.展开更多
Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between ...Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between rye and wheat chromosomes,not only introduced Yr9into wheat but also incorporated Sr31,Lr26,and Pm8,thereby forming a robust arsenal of disease-resistance genes(Mago et al.,2005).In China,the 1RS-1BL cultivars like "Aimengniu", "Lovrin 10".展开更多
Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments.Despite their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting divers...Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments.Despite their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across species.The functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains unclear.In this study,we comprehensively characterized the sequence composition and organization of rye centromeres.Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed minisatellites.We systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes.The minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in rye.Additionally,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in R-loops.Notably,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification.Our work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye centromeres.This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.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
基金the National Natural Science Foundation of China(31991212)the National Key Research and Development Program of China(2022YFF1003303).
文摘The Triticum-Aegilops complex groups demonstrated high cross-affinity with each other to overcome the barriers of distant hybridization(Loureiro et al.,2023).Distant hybridization involves two distinct yet closely related events:hybridization and genome doubling.Previous studies have indicated that bursts of transposable elements(TEs)can occur as a consequence or concomitant to hybridization or genome duplication(Parisod et al.,2010).This raises an important scientific question regarding how the TEs-rich centromere region copes with genomic shock(McClintock,1984).The Triticum-Aegilops species complexes,particularly in the F1,So,and subsequent early generations resulting from successive selfcrossing,offer an opportunity to investigate whether the centromere environment undergoes reconstruction and the associated mechanisms that maintain genomic stability.
基金supported by grants from the Biological Breeding-National Science and Technology Major Project(2024ZD04079)the National Natural Science Foundation of China(32370261).
文摘Dear Editor,Legumes,including soybean and alfalfa,are vital agricultural crops worldwide,providing high-quality protein and oil sources for humans and animals.In addition,legumes also provide nitrogen for soil improvement,benefiting from their symbiotic associations with nitrogen-fixing bacteria.
基金supported by the National Natural Science Foundation of China (NSFC31991212)the National Key Research and Development Program of China (2022YFF1003303)。
文摘Dear Editor,The 1RS-1BL translocation chromosome,carrying the stripe rust resistance gene Yr9,has shaped global wheat breeding for half a century.The 1RS-1BL translocation chromosome,derived from the exchange between rye and wheat chromosomes,not only introduced Yr9into wheat but also incorporated Sr31,Lr26,and Pm8,thereby forming a robust arsenal of disease-resistance genes(Mago et al.,2005).In China,the 1RS-1BL cultivars like "Aimengniu", "Lovrin 10".
基金supported by the National Natural Science Foundation of China(31991212,31920103006)。
文摘Centromeres play a vital role in cellular division by facilitating kinetochore assembly and spindle attachments.Despite their conserved functionality,centromeric DNA sequences exhibit rapid evolution,presenting diverse sizes and compositions across species.The functional significance of rye centromeric DNA sequences,particularly in centromere identity,remains unclear.In this study,we comprehensively characterized the sequence composition and organization of rye centromeres.Our findings revealed that these centromeres are primarily composed of long terminal repeat retrotransposons(LTR-RTs)and interspersed minisatellites.We systematically classified LTR-RTs into five categories,highlighting the prevalence of younger CRS1,CRS2,and CRS3 of CRSs(centromeric retrotransposons of Secale cereale)were primarily located in the core centromeres and exhibited a higher association with CENH3 nucleosomes.The minisatellites,mainly derived from retrotransposons,along with CRSs,played a pivotal role in establishing functional centromeres in rye.Additionally,we observed the formation of R-loops at specific regions of CRS1,CRS2,and CRS3,with both rye pericentromeres and centromeres exhibiting enrichment in R-loops.Notably,these R-loops selectively formed at binding regions of the CENH3 nucleosome in rye centromeres,suggesting a potential role in mediating the precise loading of CENH3 to centromeres and contributing to centromere specification.Our work provides insights into the DNA sequence composition,distribution,and potential function of R-loops in rye centromeres.This knowledge contributes valuable information to understanding the genetics and epigenetics of rye centromeres,offering implications for the development of synthetic centromeres in future plant modifications and beyond.
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.
