Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,w...Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,we report a high-quality reference genome of P.notoginseng,with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb,produced with third-generation PacBio sequencing technology.This is the first chromosome-level genome assembly for the genus Panax.Through genome evolution analysis,we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis.We performed a detailed transcriptional analysis of P.notoginseng and explored genelevel mechanisms that regulate the formation of characteristic tubercles.Next,we studied the biosynthesis and regulation of saponins at temporal and spatial levels.We combined multi-omics data to identify genes that encode key enzymes in the P.notoginseng terpenoid biosynthetic pathway.Finally,we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P.notoginseng.The genetic information obtained in this study provides a resource for further exploration of the growth characteristics,cultivation,breeding,and saponin biosynthesis of P.notoginseng.展开更多
Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identif...Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.展开更多
Objective: To in vestigate the relati on ship betwee n gene mutations and resp onse to Compo und Qinghuang Powder (复方青黄散,CQHP) in patients with myelodysplastic syndrome (MDS). Methods: Forty-three MDS patients af...Objective: To in vestigate the relati on ship betwee n gene mutations and resp onse to Compo und Qinghuang Powder (复方青黄散,CQHP) in patients with myelodysplastic syndrome (MDS). Methods: Forty-three MDS patients after treatment with CQHP for 6 months were genotyped by ultra-deep targeted sequencing and the clinical data of patients were collected and the relationship between them was analyzed. Results: Up to 41.86% of patie nts harbored genet mutations, in most cases with more than one mutation. The most comm on mutations were in SF3B1, U2AF1, ASXL1, and DNMT3A. After treatment with CQHP, about 88.00% of patients no longer required blood transfusion, or needed half of prior transfusions. Conlusion: CQHP is an effective treatment for patients with MDS, especially those with gene mutations in SF3B1, DNMT3A, U2AF1, and/or ASXL1.展开更多
Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and c...Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and cold areas across China.By characterizing the population structure and demographic history,we identified two genetic clusters,i.e.,northern and southern groups,as well as a common historic population peak at 30 kilo years ago.Genomic scan of cold-tolerant breeds determined potential candidate genes in the thermogenesis-related pathways that were under selection.Specifically,functional analysis identified a substitution of PRDM16(p.P779 L)in northern cattle,which maintains brown adipocyte formation by boosting thermogenesis-related gene expression,indicating a vital role of this gene in cold tolerance.These findings provide a basis for genetic variation in domestic cattle shaped by environmental temperature and highlight the role of reverse mutation in livestock species.展开更多
A reliable,efficient anther culture system,the dominant technique for generating haploid plants in breeding programs,that can be used for generating transgenic poplar plants has been needed.In the present study,theref...A reliable,efficient anther culture system,the dominant technique for generating haploid plants in breeding programs,that can be used for generating transgenic poplar plants has been needed.In the present study,therefore,an anther culture system was developed using isolated mid-and late-uninucleate anthers of poplar(Populus simonii x P.nigra).From a combination of SSR and ploidy analyses,six double haploid and two haploid lines were characterized from 86 plants grown from 16 regenerated anther cultured lines.After 48 months of development,two plant lines from the regenerated plants maintained their haploid level in vitro for over 2 years.A number of haploid plants from the different lines weretransferred to soil.The leaves of these transplants were then used as explants for transformation with the APETALA1(AP1) gene using Agrobacterium tumefaciens.Overexpression of AP1 in haploid poplar induced early flowering with obvious petals when ectopically expressed.To our knowledge,this is the first report on changes in flowering time in AP1-trangenic poplar,which is important for elucidating the regulatory mechanism of tree flower development.展开更多
Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly importa...Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique fl展开更多
The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,fe...The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109×Pacific Bio sciences(PacBio)continuous long reads(CLRs),22×PacBio circular consensus sequencing(CCS)reads,104×Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping platform,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.展开更多
Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demon...Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.展开更多
The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variati...The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.展开更多
基金support from the National Natural Science Foundation of China(nos.81891010,81891013)the Key Project at central government level:The ability establishment of sustainable use for valuable Chinese medicine resources(no.2060302-1806-03)+1 种基金the High-level Teachers in Beijing Municipal Universities in the Period of 13th Five-year Plan(no.CIT&TCD20170324)the National Program for Special Support of Eminent Professionals.
文摘Panax notoginseng,a perennial herb of the genus Panax in the family Araliaceae,has played an important role in clinical treatment in China for thousands of years because of its extensive pharmacological effects.Here,we report a high-quality reference genome of P.notoginseng,with a genome size up to 2.66 Gb and a contig N50 of 1.12 Mb,produced with third-generation PacBio sequencing technology.This is the first chromosome-level genome assembly for the genus Panax.Through genome evolution analysis,we explored phylogenetic and whole-genome duplication events and examined their impact on saponin biosynthesis.We performed a detailed transcriptional analysis of P.notoginseng and explored genelevel mechanisms that regulate the formation of characteristic tubercles.Next,we studied the biosynthesis and regulation of saponins at temporal and spatial levels.We combined multi-omics data to identify genes that encode key enzymes in the P.notoginseng terpenoid biosynthetic pathway.Finally,we identified five glycosyltransferase genes whose products catalyzed the formation of different ginsenosides in P.notoginseng.The genetic information obtained in this study provides a resource for further exploration of the growth characteristics,cultivation,breeding,and saponin biosynthesis of P.notoginseng.
基金This work was supported by the National Key R&D Program of China(Grant No.2018YFD0502204)the Agricultural Science and Technology Innovation Program of China(Grant No.CAAS-ASTIP-2019-ISAPS)+1 种基金the Special Animal Genetic Resources Platform of National Scientific and Technical Infrastructure Center(Grant No.NSTIC TZDWZYK2019)the Sika deer Genome Project of China(Grant No.20140309016YY).
文摘Sika deer are known to prefer oak leaves,which are rich in tannins and toxic to most mammals;however,the genetic mechanisms underlying their unique ability to adapt to living in the jungle are still unclear.In identifying the mechanism responsible for the tolerance of a highly toxic diet,we have made a major advancement by explaining the genome of sika deer.We generated the first high-quality,chromosome-level genome assembly of sika deer and measured the correlation between tannin intake and RNA expression in 15 tissues through 180 experiments.Comparative genome analyses showed that the UGT and CYP gene families are functionally involved in the adaptation of sika deer to high-tannin food,especially the expansion of the UGT family 2 subfamily B of UGT genes.The first chromosome-level assembly and genetic characterization of the tolerance to a highly toxic diet suggest that the sika deer genome may serve as an essential resource for understanding evolutionary events and tannin adaptation.Our study provides a paradigm of comparative expressive genomics that can be applied to the study of unique biological features in non-model animals.
基金Supported by the Beijing Municiple Science and Technology Commission(No.Z141100006014003)the National Natural Science Foundation of China(No.81673821)the Special Research Foundation of Central Level Public Scientific Research Institutes(No.ZZ10-016)
文摘Objective: To in vestigate the relati on ship betwee n gene mutations and resp onse to Compo und Qinghuang Powder (复方青黄散,CQHP) in patients with myelodysplastic syndrome (MDS). Methods: Forty-three MDS patients after treatment with CQHP for 6 months were genotyped by ultra-deep targeted sequencing and the clinical data of patients were collected and the relationship between them was analyzed. Results: Up to 41.86% of patie nts harbored genet mutations, in most cases with more than one mutation. The most comm on mutations were in SF3B1, U2AF1, ASXL1, and DNMT3A. After treatment with CQHP, about 88.00% of patients no longer required blood transfusion, or needed half of prior transfusions. Conlusion: CQHP is an effective treatment for patients with MDS, especially those with gene mutations in SF3B1, DNMT3A, U2AF1, and/or ASXL1.
基金supported by the General Program(Major Research Plan)of National Natural Science Foundation of China(92057208)National Key Research and Development Program of China(2018YFD0501702)+4 种基金Youth Program of the National Natural Science Foundation of China(31900830)National Natural Science Foundation of China(81770834)Jilin Provincial Development and Reform Commission Budget Capital Construction Fund Project(2018M640182)111 Project(D20034)China Postdoctoral Science Foundation Funded Project(2018M640182 to J.L.)。
文摘Environmental temperature serves as a major driver of adaptive changes in wild organisms.To discover the mechanisms underpinning cold tolerance in domestic animals,we sequenced the genomes of 28 cattle from warm and cold areas across China.By characterizing the population structure and demographic history,we identified two genetic clusters,i.e.,northern and southern groups,as well as a common historic population peak at 30 kilo years ago.Genomic scan of cold-tolerant breeds determined potential candidate genes in the thermogenesis-related pathways that were under selection.Specifically,functional analysis identified a substitution of PRDM16(p.P779 L)in northern cattle,which maintains brown adipocyte formation by boosting thermogenesis-related gene expression,indicating a vital role of this gene in cold tolerance.These findings provide a basis for genetic variation in domestic cattle shaped by environmental temperature and highlight the role of reverse mutation in livestock species.
基金supported by The Fundamental Research Funds for the Central Universities(2572015EA01)the Innovation Project of State Key Laboratory of Tree Genetics and Breeding(Northeast Forestry University+1 种基金grant number 2013A04)Natural Science Fund of Heilongjiang Province(No.QC2015035)
文摘A reliable,efficient anther culture system,the dominant technique for generating haploid plants in breeding programs,that can be used for generating transgenic poplar plants has been needed.In the present study,therefore,an anther culture system was developed using isolated mid-and late-uninucleate anthers of poplar(Populus simonii x P.nigra).From a combination of SSR and ploidy analyses,six double haploid and two haploid lines were characterized from 86 plants grown from 16 regenerated anther cultured lines.After 48 months of development,two plant lines from the regenerated plants maintained their haploid level in vitro for over 2 years.A number of haploid plants from the different lines weretransferred to soil.The leaves of these transplants were then used as explants for transformation with the APETALA1(AP1) gene using Agrobacterium tumefaciens.Overexpression of AP1 in haploid poplar induced early flowering with obvious petals when ectopically expressed.To our knowledge,this is the first report on changes in flowering time in AP1-trangenic poplar,which is important for elucidating the regulatory mechanism of tree flower development.
基金the National Key R&D Program of China(2022YFE0140800)the European Union Horizon 2020 project ECOBREED(771367)+4 种基金the Youth Innovation Program of Chinese Academy of Agricultural Sciences(No.Y2022QC02)Project of Sanya Yazhou Bay Science and Technology City(SCKJ-JYRC-2022-22)National Natural Science Foundation of China(32161143005,31911530772,32111540258)PlantaSYST(SGA No 739582 under FPA No.664620)the BG05M2OP001-1.003-001-C01 project,financed by the European Regional Development Fund through the“Science and Education for Smart Growth”Operational Programme and Slovenian Research Agency,program P4-0077“Genetics and Modern Technologies of Crops”.
文摘Common buckwheat(Fagopyrum esculentum)is an ancient crop with a world-wide distribution.Due to its excellent nutritional quality and high economic and ecological value,common buckwheat is becoming increasingly important throughout the world.The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat,but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly.Here we report the assembly of a chromosome-scale high-quality reference genome of F.esculentum var.homotropicum,a homozygous self-pollinating variant of common buckwheat.Comparative genomics revealed that two cultivated buckwheat species,common buckwheat(F.esculentum)and Tartary buckwheat(F.tataricum),underwent metabolomic divergence and ecotype differentiation.The expansion of several gene families in common buckwheat,including FhFAR genes,is associated with its wider distribution than Tartary buckwheat.Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat.Furthermore,we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat.Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups.Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period,a key agronomic trait controlling the yield of outcrossing crops,and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids.Intriguingly,we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat.Collectively,our results elucidate the genetic basis of speciation,ecological adaptation,fertility,and unique fl
基金supported by grants from the National Key R&D Program of China(Grant No.2017YFC0906501)。
文摘The importance of structural variants(SVs)for human phenotypes and diseases is now recognized.Although a variety of SV detection platforms and strategies that vary in sensitivity and specificity have been developed,few benchmarking procedures are available to confidently assess their performances in biological and clinical research.To facilitate the validation and application of these SV detection approaches,we established an Asian reference material by characterizing the genome of an Epstein-Barr virus(EBV)-immortalized B lymphocyte line along with identified benchmark regions and high-confidence SV calls.We established a high-confidence SV callset with 8938 SVs by integrating four alignment-based SV callers,including 109×Pacific Bio sciences(PacBio)continuous long reads(CLRs),22×PacBio circular consensus sequencing(CCS)reads,104×Oxford Nanopore Technologies(ONT)long reads,and 114×Bionano optical mapping platform,and one de novo assembly-based SV caller using CCS reads.A total of 544 randomly selected SVs were validated by PCR amplification and Sanger sequencing,demonstrating the robustness of our SV calls.Combining trio-binning-based haplotype assemblies,we established an SV benchmark for identifying false negatives and false positives by constructing the continuous high-confidence regions(CHCRs),which covered 1.46 gigabase pairs(Gb)and 6882 SVs supported by at least one diploid haplotype assembly.Establishing high-confidence SV calls for a benchmark sample that has been characterized by multiple technologies provides a valuable resource for investigating SVs in human biology,disease,and clinical research.
基金supported by the National Natural Science Foundation of China (31621062)Strategic Priority Research Program of the Chinese Academy of Sciences (XDA2004010302)+4 种基金Second Tibetan Plateau Scientific Expedition and Research (STEP)Program (2019QZKK05010703)supported by the National Natural Science Foundation of China (91731304, 31822048)Strategic Priority Research Program of the Chinese Academy of Sciences (XDB13020600)Qinghai Department of Science and Technology Major ProjectState Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan,Yunnan University(2018KF001)supported by the Animal Branch of the Germplasm Bank of Wild Species,Chinese Academy of Sciences (Large Research Infrastructure Funding)
文摘Over the last several hundred years,donkeys have adapted to high-altitude conditions on the Tibetan Plateau.Interestingly,the kiang,a closely related equid species,also inhabits this region.Previous reports have demonstrated the importance of specific genes and adaptive introgression in divergent lineages for adaptation to hypoxic conditions on the Tibetan Plateau.Here,we assessed whether donkeys and kiangs adapted to the Tibetan Plateau via the same or different biological pathways and whether adaptive introgression has occurred.We assembled a de novo genome from a kiang individual and analyzed the genomes of five kiangs and 93 donkeys(including 24 from the Tibetan Plateau).Our analyses suggested the existence of a strong hard selective sweep at the EPAS1 locus in kiangs.In Tibetan donkeys,however,another gene,i.e.,EGLN1,was likely involved in their adaptation to high altitude.In addition,admixture analysis found no evidence for interspecific gene flow between kiangs and Tibetan donkeys.Our findings indicate that despite the short evolutionary time scale since the arrival of donkeys on the Tibetan Plateau,as well as the existence of a closely related species already adapted to hypoxia,Tibetan donkeys did not acquire adaptation via admixture but instead evolved adaptations via a different biological pathway.
基金This work was supported by grants from the National Natural Science Foundation of China(31525003,31930007)to C.Y.H.grants(31970346)to H.Z.W.+1 种基金the Strategic Priority Research Program of the Chinese Academy of Sciences(XDB27010106)to C.Y.H.grants from the National Natural Science Foundation of China(31470407)to H.Z.W.
文摘The fruits of Physalis(Solanaceae)have a unique structure,a lantern-like fruiting calyx known as inflated calyx syndrome(ICS)or the Chinese lantern,and are rich in steroid-related compounds.However,the genetic variations underlying the origin of these characteristic traits and diversity in Physalis remain largely unknown.Here,we present a high-quality chromosome-level reference genome assembly of Physalis floridana(~1.40Gb in size)with a contig N50 of~4.87Mb.Through evolutionary genomics and experimental approaches,we found that the loss of the SEP-like MADS-box gene MBP21 subclade is likely a key mutation that,together with the previously revealed mutation affecting floral MPF2 expression,might have contributed to the origination of ICS in Physaleae,suggesting that the origination of a morphological novelty may have resulted from an evolutionary scenario in which one mutation compensated for another deleterious mutation.Moreover,the significant expansion of squalene epoxidase genes is potentially associated with the natural variation of steroid-related compounds in Physalis fruits.The results reveal the importance of gene gains(duplication)and/or subsequent losses as genetic bases of the evolution of distinct fruit traits,and the data serve as a valuable resource for the evolutionary genetics and breeding of solanaceous crops.
