Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid b...Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.展开更多
We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis （PFGE） over a nine-month period （April-December 2005） at ...We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis （PFGE） over a nine-month period （April-December 2005） at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphouiridae or were untailed, with capsid sizes ranging from 30 to 60 nm, and exhibited genome sizes ranging from 15 to 45 kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer （mean = 14 bands per PFGE fingerprint） and in the epilimnion （mean = 13 bands per PFGE fingerprint）. Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.展开更多
Objective: The self cross colonial prochordate, Botryllus schlosseri ( B.schlosseri ) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rat...Objective: The self cross colonial prochordate, Botryllus schlosseri ( B.schlosseri ) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B. schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods: AFLP markers are extremely sensitive to even small sequence variation, using PCR and high resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% polymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2, F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southern hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion: These results suggest that there are high frequency of polymorphic loci and mutation in genome of B. schlosseri. Gene deletion or low diversity may be the reason for high rate of death of the offspring of inbred laboratory reared strains.展开更多
The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecula...The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.展开更多
Hepatitis E virus(HEV)is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis.Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of t...Hepatitis E virus(HEV)is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis.Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential.In this study,we tested 278 specimens collected from seven wild small mammal species in Yunnan province,China,for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription(RT)-PCR.HEV-related sequences were detected in two rodent species,including Chevrier’s field mouse(Apodemus chevrieri,family Muridae)and Père David’s vole(Eothenomys melanogaster,family Cricetidae),with the infection rates of 29.20%(59/202)and 7.27%(4/55),respectively.Further four representative full-length genomes were generated:two each from Chevrier’s field mouse(named Rd HEVAc14 and Rd HEVAc86)and Père David’s vole(Rd HEVEm40 and Rd HEVEm67).Phylogenetic analyses and pairwise distance comparisons of whole genome sequences and amino acid sequences of the gene coding regions showed that orthohepeviruses identified in Chinese Chevrier’s field mouse and Père David’s vole belonged to the species Orthohepevirus C but were highly divergent from the two assigned genotypes:HEV-C1 derived from rat and shrew,and HEV-C2 derived from ferret and possibly mink.Quantitative real-time RT-PCR demonstrated that these newly discovered orthohepeviruses had hepatic tropism.In summary,our work discovered two putative novel genotypes orthohepeviruses preliminarily named HEVC3 and HEV-C4 within the species Orthohepevirus C,which expands our understanding of orthohepevirus infection in the order Rodentia and gives new insights into the origin,evolution,and host range of orthohepevirus.展开更多
Genomic sources from China are underrepresented in the population-specific reference database.We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups...Genomic sources from China are underrepresented in the population-specific reference database.We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups(1,081 Sinitic,56 Mongolic,40 Turkic,and 30Tibeto-Burman people)living in North China included in the 10K Chinese People Genomic Diversity Project(10K_CPGDP)to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China.We observed a population split between Northwest Chinese minorities(NWCMs)and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs.The observed population substructures among ethnically/linguistically diverse NWCMs suggested that differentiated admixture events contributed to the differences in their genomic and phenotypic diversity.We estimated that the Dongxiang,Tibetan,and Yugur people inherited more than 10%of the Western Eurasian ancestry,which is much greater than that of the Salar and Tu people(<7%),while Han neighbors showed less West Eurasian ancestry(~1%-3%).Male-biased admixture introduced Western Eurasian ancestry in the Dongxiang,Tibetan,and Yugur populations.We found that the eastern-western admixture in NWCMs occurred~800-1,100 years ago,coinciding with intensive economic and cultural exchanges during the Tang and Song dynasties.Additionally,we identified the signatures of natural selection associated with cardiovascular system diseases or lipid metabolism and developmental/neurogenetic disorders.Moreover,the EPAS1 gene showed relatively high population branch statistic values in NWCMs.The well-fitted demographical models presented the vast landscape of complex admixture processes of the Silk Road people,and the newly reported functionally important variations suggested the importance of including ethnolinguistically diverse populations in Chinese genetic studies for uncovering the genetic basis of complex traits/diseases.展开更多
Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable c...Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.展开更多
Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making g...Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.展开更多
Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways wi...Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways with organisms of Bacteria, the sister prokaryotic phylum. Archaeal organisms also possess unique features as revealed by genomics and genome comparisons and by biochemical characterization of prominent enzymes. Nevertheless, diverse genetic tools are required for in vivo experiments to verify these interesting discoveries. Considerable efforts have been devoted to the development of genetic tools for archaea ever since their discovery, and great progress has been made in the creation of archaeal genetic tools in the past decade. Versatile genetic toolboxes are now available for several archaeal models, among which Sulfolobus microorganisms are the only genus representing Crenarchaeota because all the remaining genera are from Euryarchaeota. Nevertheless, genetic tools developed for Sulfolobus are probably the most versatile among all archaeal models, and these include viral and plasmid shuttle vectors, conventional and novel genetic manipulation methods, CRISPR-based gene deletion and mutagenesis, and gene silencing, among which CRISPR tools have been reported only for Sulfolobus thus far. In this review, we summarize recent developments in all these useful genetic tools and discuss their possible application to research into archaeal biology by means of Sulfolobus models.展开更多
基金supported by the Italian Ministry of Agriculture,Food Sovereignty and Forests(project GOOD-MILK,D.M.9367185—09/12/2020,CUP C29C20000450001,Roma,Italy)the Regional Government of Sardinia(Progetto Strategico Sulcis,CUP J73C17000070007,Cagliari,Italy).
文摘Background Goat breeds in the Alpine area and Mediterranean basin exhibit a unique genetic heritage shaped by centuries of selection and adaptability to harsh environments.Understanding their adaptive traits can aid breeding programs target enhanced resilience and productivity,especially as we are facing important climate and agriculture challenges.To this aim the genomic architecture of 480 goats belonging to five breeds(i.e.,Saanen[SAA],Camosciata delle Alpi[CAM],Murciano-Granadina[MUR],Maltese[MAL],Sarda[SAR])reared in the Sardinia Island were genotyped and their genomic architecture evaluated to find molecular basis of adaptive traits.Inbreeding,runs of homozygosity(ROH)and runs of heterozygosity(ROHet)were identified.Finally,candidate genes in the ROH and ROHet regions were explored through a pathway analysis to assess their molecular role.Results In total,we detected 10,341 ROH in the SAA genome,11,063 ROH in the CAM genome,12,250 ROH in the MUR genome,8,939 ROH in the MAL genome,and 18,441 ROH in the SAR genome.Moreover,we identified 4,087 ROHet for SAA,3,360 for CAM,2,927 for MUR,3,701 for MAL,and 3,576 for SAR,with SAR having the highest heterozygosity coefficient.Interestingly,when computing the inbreeding coefficient using homozygous segment(FROH),SAA showed the lowest value while MAL the highest one,suggesting the need to improve selecting strategies to preserve genetic diversity within the population.Among the most significant candidate genes,we identified several ones linked to different physiological functions,such as milk production(e.g.,DGAT1,B4GALT1),immunity(GABARAP,GPS2)and adaptation to environment(e.g.,GJA3,GJB2 and GJB6).Conclusions This study highlighted the genetic diversity within and among five goat breeds.The high levels of ROH identified in some breeds might indicate high levels of inbreeding and a lack in genetic variation,which might negatively impact the animal population.Conversely,high levels of ROHet might indicate regions of the genetic diversity,beneficial for breed health and resilience.Therefore,these findings could aid breeding programs in managing inbreeding and preserving genetic diversity.
基金supported by a PhD Fellowship from the Grand Duchédu Luxembourg(BFR04/047,Ministry of Culture,High School,and Research)supported by the French National Program ACI/FNS“ECCO”(VIRULAC research grant awarded to TSN,coordinator)the French ANR Program“Biodiversité”(AQUAPHAGE research grant to TSN,PI)
文摘We examined changes in morphological and genomic diversities of viruses by means of transmission electronic microscopy and pulsed field gel electrophoresis （PFGE） over a nine-month period （April-December 2005） at four different depths in the oligomesotrophic Lac Pavin. We found that the majority of viruses in this lake belonged to the family of Siphouiridae or were untailed, with capsid sizes ranging from 30 to 60 nm, and exhibited genome sizes ranging from 15 to 45 kb. On average, 12 different genotypes dominated each of the PFGE fingerprints. The highest genomic viral richness was recorded in summer （mean = 14 bands per PFGE fingerprint） and in the epilimnion （mean = 13 bands per PFGE fingerprint）. Among the physico-chemical and biological variables considered, the availability of the hosts appeared to be the main factor regulating the variations in the viral diversity.
文摘Objective: The self cross colonial prochordate, Botryllus schlosseri ( B.schlosseri ) occupy a key phylogenetic position in the evolution of vertebrates. To clarify the relationship of genome diversity and survive rate, five generations of B. schlosseri was investigated by amplified fragment length polymorphism (AFLP). Methods: AFLP markers are extremely sensitive to even small sequence variation, using PCR and high resolution electrophoresis to examine restriction fragments. Results: AFLP polymorphism was high in the parent and lower in its F1, F2, F3 and F4. Each primer combination generated from 80 to more than 120 bands, of which average 25.85% polymorphic loci in parent, 15.79% polymorphic among F1, 9.16% and 5.58% in F2, F3. The AFLP markers were transmitted from F1 to F2, F3 and F4 and inherited, segregated in expected Mendelian ratio. However, some of the markers were lost in F2, F3 and F4 while it disappeared in their mother. In addition, gene mutation new loci and lost loci among F1, F2, F3 and F4 were observed. These special fragments were cloned and sequenced. Then, the genomic DNA was analyzed by Southern hybridization with the probes from these specific fragments and the mechanism of gene mutation was clarified. Conclusion: These results suggest that there are high frequency of polymorphic loci and mutation in genome of B. schlosseri. Gene deletion or low diversity may be the reason for high rate of death of the offspring of inbred laboratory reared strains.
基金supported by the Ministry of Science and Higher Education of the Russian Federation(No.075-152021-1037,Internal No.15.BRK.21.0001)。
文摘The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse origin.This study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 populations.These populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried out.This included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population size.It also included assessment of linkage disequilibrium and construction of phylogenetic trees.Using multidimensional scaling,principal component analysis,and ADMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each breed.An overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous breeds.Such a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry breeding.In general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.
基金the National Natural Science Foundation of China (81660558,81260437,and 81290341)a Scientific and Technological Basis Special Project grant (2013FY113500) from the Ministry of Science and Technology of PR China+1 种基金Yunnan Provincial Collaborative Innovation Centre for Public Health and Disease Prevention and Control (2015YNPHXT05)the China Scholarship Council (CSC),Beijing,China
文摘Hepatitis E virus(HEV)is the prototype of the family Hepeviridae and the causative agent of common acute viral hepatitis.Genetically diverse HEV-related viruses have been detected in a variety of mammals and some of them may have zoonotic potential.In this study,we tested 278 specimens collected from seven wild small mammal species in Yunnan province,China,for the presence and prevalence of orthohepevirus by broad-spectrum reverse transcription(RT)-PCR.HEV-related sequences were detected in two rodent species,including Chevrier’s field mouse(Apodemus chevrieri,family Muridae)and Père David’s vole(Eothenomys melanogaster,family Cricetidae),with the infection rates of 29.20%(59/202)and 7.27%(4/55),respectively.Further four representative full-length genomes were generated:two each from Chevrier’s field mouse(named Rd HEVAc14 and Rd HEVAc86)and Père David’s vole(Rd HEVEm40 and Rd HEVEm67).Phylogenetic analyses and pairwise distance comparisons of whole genome sequences and amino acid sequences of the gene coding regions showed that orthohepeviruses identified in Chinese Chevrier’s field mouse and Père David’s vole belonged to the species Orthohepevirus C but were highly divergent from the two assigned genotypes:HEV-C1 derived from rat and shrew,and HEV-C2 derived from ferret and possibly mink.Quantitative real-time RT-PCR demonstrated that these newly discovered orthohepeviruses had hepatic tropism.In summary,our work discovered two putative novel genotypes orthohepeviruses preliminarily named HEVC3 and HEV-C4 within the species Orthohepevirus C,which expands our understanding of orthohepevirus infection in the order Rodentia and gives new insights into the origin,evolution,and host range of orthohepevirus.
基金supported by the National Natural Science Foundation of China(82402203,82202078)the Major Project of the National Social Science Foundation of China(23&ZD203)+3 种基金the Open Project of the Key Laboratory of Forensic Genetics of the Ministry of Public Security(2022FGKFKT05,2024FGKFKT02)the Center for Archaeological Science of Sichuan University(23SASA01)the 1·3·5 Project for Disciplines of Excellence,West China Hospital,Sichuan University(ZYJC20002)the Sichuan Science and Technology Program(2024NSFSC1518)。
文摘Genomic sources from China are underrepresented in the population-specific reference database.We performed whole-genome sequencing or genome-wide genotyping on 1,207 individuals from four linguistically diverse groups(1,081 Sinitic,56 Mongolic,40 Turkic,and 30Tibeto-Burman people)living in North China included in the 10K Chinese People Genomic Diversity Project(10K_CPGDP)to characterize the genetic architecture and adaptative history of ethnic groups in the Silk Road Region of China.We observed a population split between Northwest Chinese minorities(NWCMs)and Han Chinese since the Upper Paleolithic and later Neolithic genetic differentiation within NWCMs.The observed population substructures among ethnically/linguistically diverse NWCMs suggested that differentiated admixture events contributed to the differences in their genomic and phenotypic diversity.We estimated that the Dongxiang,Tibetan,and Yugur people inherited more than 10%of the Western Eurasian ancestry,which is much greater than that of the Salar and Tu people(<7%),while Han neighbors showed less West Eurasian ancestry(~1%-3%).Male-biased admixture introduced Western Eurasian ancestry in the Dongxiang,Tibetan,and Yugur populations.We found that the eastern-western admixture in NWCMs occurred~800-1,100 years ago,coinciding with intensive economic and cultural exchanges during the Tang and Song dynasties.Additionally,we identified the signatures of natural selection associated with cardiovascular system diseases or lipid metabolism and developmental/neurogenetic disorders.Moreover,the EPAS1 gene showed relatively high population branch statistic values in NWCMs.The well-fitted demographical models presented the vast landscape of complex admixture processes of the Silk Road people,and the newly reported functionally important variations suggested the importance of including ethnolinguistically diverse populations in Chinese genetic studies for uncovering the genetic basis of complex traits/diseases.
基金supported by the Laoshan Laboratory(LSKJ202203203)the National Natural Science Foundation of China(31961123002,32270435 and 32471688)+1 种基金the National Institutes of Health(R35-GM122566-01)the National Science Foundation(DBI-2119963,DEB-1927159 and 1911449).
文摘Paramecium,a group of ciliates with a long evolutionary history,plays essential roles in freshwater ecosystems and has been model for genetic,cellular,and evolutionary studies for over a century.Despite the valuable contributions of genomic resources such as ParameciumDB,genomic data are still mostly limited to species in and near the P.aurelia group.This study addresses this gap by HiFi sequencing,assembling,and annotating the macronuclear genomes of five rare Paramecium species:P.calkinsi,P.duboscqui,P.nephridiatum,P.putrinum,and P.woodruffi.These genomes enable a comprehensive exploration of genomic diversity,genome evolution,and phylogenomic relationships within the genus Paramecium.The genome sizes range from 47.78 to 113.16 Mb,reflecting unexpected variation in genomic content,and genic features differ from those of other reported Paramecium genomes,such as larger intron sizes and higher GC content.Nonetheless,the de novo assemblies indicate that macronuclear genomes of all Paramecium are highly streamlined,with~77%being protein-coding gene regions.Based on gene-duplication depths,synonymous mutations in paralogs,and phylogenomic relationships,we discovered that the five species experienced at least three whole-genome duplication(WGD)events,independent of those previously found in the P.aurelia complex.Using all available WGD data for Paramecium,we further explore the paralog dynamics after WGD events by modeling.This study contributed to a more comprehensive and deeper understanding of genome architecture and evolution in Paramecium.
基金support from the Youth Innovation Promotion Association of the Chinese Academy of Sciences,China (Grant No.2017141) awarded to SSthe Strategic Priority Research Program (Grant No.XDA08010304)+1 种基金Key Research Program of Frontier Sciences (Grant No.QYZDY-SSW-SMC017)R&D Projects of Scientific Research Equipment Programs (Grant Nos.YZ201568 and YZ201402) of the Chinese Academy of Sciences,China awarded to JY
文摘Domestic rice(Oryza sativa L.) is one of the most important cereal crops, feeding a large number of worldwide populations. Along with various high-throughput genome sequencing projects, rice genomics has been making great headway toward direct ?eld applications of basic research advances in understanding the molecular mechanisms of agronomical traits and utilizing diverse germplasm resources. Here, we brie?y review its achievements over the past two decades and present the potential for its bright future.
基金supported by the Danish Council of Independent Research (DFF-0602-02196, DFF-4181-00274, DFF-1323-00330)the Fundamental Research Funds for the Central Universities (2662015PX199)
文摘Archaea represents the third domain of life, with the information-processing machineries more closely resembling those of eukaryotes than the machineries of the bacterial counterparts but sharing metabolic pathways with organisms of Bacteria, the sister prokaryotic phylum. Archaeal organisms also possess unique features as revealed by genomics and genome comparisons and by biochemical characterization of prominent enzymes. Nevertheless, diverse genetic tools are required for in vivo experiments to verify these interesting discoveries. Considerable efforts have been devoted to the development of genetic tools for archaea ever since their discovery, and great progress has been made in the creation of archaeal genetic tools in the past decade. Versatile genetic toolboxes are now available for several archaeal models, among which Sulfolobus microorganisms are the only genus representing Crenarchaeota because all the remaining genera are from Euryarchaeota. Nevertheless, genetic tools developed for Sulfolobus are probably the most versatile among all archaeal models, and these include viral and plasmid shuttle vectors, conventional and novel genetic manipulation methods, CRISPR-based gene deletion and mutagenesis, and gene silencing, among which CRISPR tools have been reported only for Sulfolobus thus far. In this review, we summarize recent developments in all these useful genetic tools and discuss their possible application to research into archaeal biology by means of Sulfolobus models.
