Human embryonic stem cells(hESCs)can be classified as having naive and primed pluripotency states.While several studies have reported different gene expression networks between these two pluripotency states,the role o...Human embryonic stem cells(hESCs)can be classified as having naive and primed pluripotency states.While several studies have reported different gene expression networks between these two pluripotency states,the role of alternative splicing(AS)in regulating these differences has not been well characterized.In this study,we performed RNA sequencing and identified differential AS events in 784 genes between naive and primed hESCs.Among these,KIAA1522,whose function has not been well studied,has state-specific isoforms regulated by alternative first exon(AFE).This splicing event resulted in isoforms with distinct N-terminal domains and subcellular localization.Notably,the sequences and alternative isoform patterns of KIAA1522 were conserved between humans and mice.Further investigation using cleavage under targets and tagmentation(CUT&Tag)experiments in cells with specific-isoform overexpression or knockdown revealed the opposite activity of long terminal repeat retrotransposons(LTR-RTs)and motif enrichment profiles.The naive-specific(N-P)isoform upregulated naive marker gene expression and preferentially activated LTR-RTs by binding to the motifs enriched for POU and FOX family transcription factor binding sites.Conversely,the primed-specific(P-P)isoform promoted primed marker gene expression and suppressed LTR-RTs activity by binding to the motifs enriched for zinc finger protein binding sites.Collectively,KIAA1522 regulates the balance between naive and primed pluripotency states through isoform-specific regulation of LTR-RTs activity and collaboration with distinct transcriptional regulators.In summary,our results characterize the splicing atlas of hESCs in naive and primed states and reveal the regulatory function and mechanism of AFE usage by KIAA1522.展开更多
Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified ...Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene(named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene,GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis,also has potential breeding value by engineering GaPC to develop colored petals or fibers for multifunctional utilization of cotton.展开更多
Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on h...Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs.However,for non-model species,this remains a challenge.To address this,we developed LTR_Stream for sublineage clustering of LTR-RTs in specific or closely related species,providing higher precision than current database-based lineage-level clustering.Using LTR_Stream,we analyzed Retand LTR-RTs in three Papaver species.Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome.For instance,we found that autonomous Retand elements could spread among the ancestors of different subgenomes,like retroviral pandemics,enriching genetic diversity.Additionally,we identified that specific truncated fragments containing transcription factor motifs such as TCP and bZIP may contribute to the generation of novel topologically associating domain-like(TAD-like)boundaries.Notably,our preallopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization,suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs.We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.展开更多
Astragalus membranaceus var.mongholicus(AMM),a member of the Leguminosae,is one of the most important medicinal plants worldwide.The dried roots of AMM have a wide range of pharmacological effects and are a traditiona...Astragalus membranaceus var.mongholicus(AMM),a member of the Leguminosae,is one of the most important medicinal plants worldwide.The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine.Here,we report the first chromosome-level reference genome of AMM,comprising nine pseudochromosomes with a total size of 1.47 Gb and 27868 protein-encoding genes.Comparative genomic analysis reveals that AMM has not experienced an independent wholegenome duplication(WGD)event after the WGD event shared by the Papilionoideae species.Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago,which may explain the large size of the AMM genome.Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded,and our data indicate that tandemduplication has been the main driver for expansion of these families.Among the expanded families,the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM,suggesting their roles in the biosynthesis of phenylpropanoid compounds.The functional versatility of 2,3-oxidosqualene cyclase genes in cluster Ⅲ may play a critical role in the diversification of triterpenoids in AMM.Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.展开更多
Cultivated hawthorn(Crataegus pinnatifida var.major)is an important medicinal and edible plant with a long history of use for health protection in China.Herein,we provide a de novo chromosomelevel genome sequence of t...Cultivated hawthorn(Crataegus pinnatifida var.major)is an important medicinal and edible plant with a long history of use for health protection in China.Herein,we provide a de novo chromosomelevel genome sequence of the hawthorn cultivar“Qiu Jinxing.”We assembled an 823.41 Mb genome encoding 40571 genes and further anchored the779.24 Mb sequence into 17 pseudo-chromosomes,which account for 94.64%of the assembled genome.Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae(apple tribe)at approximately 35.4 Mya.Notably,genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome.In addition,our results indicated that the Maleae share a unique ancient tetraploidization event;however,no recent independent whole-genome duplication event was specifically detected in hawthorn.The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome.Furthermore,we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms.We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleopolyploid origin patterns(autopolyploidization or allopolyploidization)of Maleae.Overall,our study provides an improved context for understanding the evolution of Maleae species,and this new highquality reference genome provides a useful resource for the horticultural improvement of hawthorn.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
基金supported by the National Key Research and Development Program of China(2023YFA1802000,2022YFA1104100,2018YFA0109700,2018YFE0201102,2019YFA0110000)Strategic Priority Research Program of the Chinese Academy of Sciences(XDA16010503)+4 种基金the Youth Innovation Promotion Association,CAS(Y2023020)the National Natural Science Foundation of China(62127811)Strategic Collaborative Research Program of the Ferring Institute of Reproductive Medicine,Ferring Pharmaceuticals,Chinese Academy of Sciences(FIRMD181101)Informatization Plan of Chinese Academy of Sciences(CAS-WX2021SF-0101)Initiative Scientific Research Program,Institute of Zoology,Chinese Academy of Sciences(2023IOZ0302)。
文摘Human embryonic stem cells(hESCs)can be classified as having naive and primed pluripotency states.While several studies have reported different gene expression networks between these two pluripotency states,the role of alternative splicing(AS)in regulating these differences has not been well characterized.In this study,we performed RNA sequencing and identified differential AS events in 784 genes between naive and primed hESCs.Among these,KIAA1522,whose function has not been well studied,has state-specific isoforms regulated by alternative first exon(AFE).This splicing event resulted in isoforms with distinct N-terminal domains and subcellular localization.Notably,the sequences and alternative isoform patterns of KIAA1522 were conserved between humans and mice.Further investigation using cleavage under targets and tagmentation(CUT&Tag)experiments in cells with specific-isoform overexpression or knockdown revealed the opposite activity of long terminal repeat retrotransposons(LTR-RTs)and motif enrichment profiles.The naive-specific(N-P)isoform upregulated naive marker gene expression and preferentially activated LTR-RTs by binding to the motifs enriched for POU and FOX family transcription factor binding sites.Conversely,the primed-specific(P-P)isoform promoted primed marker gene expression and suppressed LTR-RTs activity by binding to the motifs enriched for zinc finger protein binding sites.Collectively,KIAA1522 regulates the balance between naive and primed pluripotency states through isoform-specific regulation of LTR-RTs activity and collaboration with distinct transcriptional regulators.In summary,our results characterize the splicing atlas of hESCs in naive and primed states and reveal the regulatory function and mechanism of AFE usage by KIAA1522.
基金supported by the Fundamental Research Funds for the Central Universities(KYZZ2022003)Jiangsu Collaborative Innovation Center for Modern Crop Production project (No.10)。
文摘Although a few cases of genetic epistasis in plants have been reported, the combined analysis of genetically phenotypic segregation and the related molecular mechanism remains rarely studied. Here, we have identified a gene(named GaPC) controlling petal coloration in Gossypium arboreum and following a heritable recessive epistatic genetic model. Petal coloration is controlled by a single dominant gene,GaPC. A loss-of-function mutation of GaPC leads to a recessive gene Gapc that masks the phenotype of other color genes and shows recessive epistatic interactions. Map-based cloning showed that GaPC encodes an R2R3-MYB transcription factor. A 4814-bp long terminal repeat retrotransposon insertion at the second exon led to GaPC loss of function and disabled petal coloration. GaPC controlled petal coloration by regulating the anthocyanin and flavone biosynthesis pathways. Expression of core genes in the phenylpropanoid and anthocyanin pathways was higher in colored than in white petals. Petal color was conferred by flavonoids and anthocyanins, with red and yellow petals rich in anthocyanin and flavonol glycosides, respectively. This study provides new insight on molecular mechanism of recessive epistasis,also has potential breeding value by engineering GaPC to develop colored petals or fibers for multifunctional utilization of cotton.
基金supported by the National Key R&D Program of China(Grant No.2022YFC3400300 to Kai Ye and Xiaofei Yang)the National Natural Science Foundation of China(Grant Nos.32125009 to Kai Ye,32070663 to Kai Ye,62172325 to Xiaofei Yang,and 32422019 to Xiaofei Yang)+2 种基金the Natural Science Foundation of Shaanxi Province(Grant No.2024JC-JCQN-28 to Xiaofei Yang)the Fundamental Research Funds for the Central Universities(Grant No.xzy012024088 to Xiaofei Yang)Funding for open access charge:National Key R&D Program of China.
文摘Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs.However,for non-model species,this remains a challenge.To address this,we developed LTR_Stream for sublineage clustering of LTR-RTs in specific or closely related species,providing higher precision than current database-based lineage-level clustering.Using LTR_Stream,we analyzed Retand LTR-RTs in three Papaver species.Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome.For instance,we found that autonomous Retand elements could spread among the ancestors of different subgenomes,like retroviral pandemics,enriching genetic diversity.Additionally,we identified that specific truncated fragments containing transcription factor motifs such as TCP and bZIP may contribute to the generation of novel topologically associating domain-like(TAD-like)boundaries.Notably,our preallopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization,suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs.We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.
基金supported by grants from the City-University Cooperation Project of China(201904710111639).
文摘Astragalus membranaceus var.mongholicus(AMM),a member of the Leguminosae,is one of the most important medicinal plants worldwide.The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine.Here,we report the first chromosome-level reference genome of AMM,comprising nine pseudochromosomes with a total size of 1.47 Gb and 27868 protein-encoding genes.Comparative genomic analysis reveals that AMM has not experienced an independent wholegenome duplication(WGD)event after the WGD event shared by the Papilionoideae species.Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago,which may explain the large size of the AMM genome.Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded,and our data indicate that tandemduplication has been the main driver for expansion of these families.Among the expanded families,the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM,suggesting their roles in the biosynthesis of phenylpropanoid compounds.The functional versatility of 2,3-oxidosqualene cyclase genes in cluster Ⅲ may play a critical role in the diversification of triterpenoids in AMM.Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
基金supported by grants from National Natural Science Foundation of China(32060237 to T.Z.and 32060085 to Q.Q.)funding from the European Research Council(ERC)under the European Union’s Horizon 2020 research and innovation program(No.833522)from Ghent University(Methusalem funding,BOF.MET.2021.0005.01)。
文摘Cultivated hawthorn(Crataegus pinnatifida var.major)is an important medicinal and edible plant with a long history of use for health protection in China.Herein,we provide a de novo chromosomelevel genome sequence of the hawthorn cultivar“Qiu Jinxing.”We assembled an 823.41 Mb genome encoding 40571 genes and further anchored the779.24 Mb sequence into 17 pseudo-chromosomes,which account for 94.64%of the assembled genome.Phylogenomic analyses revealed that cultivated hawthorn diverged from other species within the Maleae(apple tribe)at approximately 35.4 Mya.Notably,genes involved in the flavonoid and triterpenoid biosynthetic pathways have been significantly amplified in the hawthorn genome.In addition,our results indicated that the Maleae share a unique ancient tetraploidization event;however,no recent independent whole-genome duplication event was specifically detected in hawthorn.The amplification of non-specific long terminal repeat retrotransposons contributed the most to the expansion of the hawthorn genome.Furthermore,we identified two paleo-sub-genomes in extant species of Maleae and found that these two sub-genomes showed different rearrangement mechanisms.We also reconstructed the ancestral chromosomes of Rosaceae and discussed two possible paleopolyploid origin patterns(autopolyploidization or allopolyploidization)of Maleae.Overall,our study provides an improved context for understanding the evolution of Maleae species,and this new highquality reference genome provides a useful resource for the horticultural improvement of hawthorn.
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.
