Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally c...Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental conditions.Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production type.Results We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important traits.Most candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment analysis.Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.展开更多
Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined ...Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions,thus limiting their ability to expand into novel environments.However,the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood.The Niviventer niviventer species complex(NNSC),consisting of highly abundant wild rats in Southeast Asia and China,offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related.In the present study,we combined ecological niche modeling with phylogenetic analysis,which suggested that sister species cannot be both widespread and dominant within the same geographical region.Moreover,by assessing heterozygosity,linkage disequilibrium decay,and Tajima's D analysis,we found that widespread species exhibited higher genetic diversity than narrow-range species.In addition,by exploring the“genomic islands of speciation”,we identified 13 genes in highly divergent regions that were shared by the two widespread species,distinguishing them from their narrow-range counterparts.Functional annotation analysis indicated that these genes are involved in nervous system development and regulation.The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.展开更多
【目的】研究bla_(CMY-2)阳性禽源奇异变形杆菌的多重耐药特征,并分析菌株CY32全基因组序列结构。【方法】对5株bla_(CMY-2)阳性禽源奇异变形杆菌进行氟苯尼考和质粒介导氟喹诺酮类耐药基因检测、接合试验和bla_(CMY-2)基因的Southern...【目的】研究bla_(CMY-2)阳性禽源奇异变形杆菌的多重耐药特征,并分析菌株CY32全基因组序列结构。【方法】对5株bla_(CMY-2)阳性禽源奇异变形杆菌进行氟苯尼考和质粒介导氟喹诺酮类耐药基因检测、接合试验和bla_(CMY-2)基因的Southern杂交定位,对其中一株菌CY32进行全基因测序和生物信息学分析。【结果】5株奇异变形杆菌携带的bla_(CMY-2)位于染色体,其中,菌株CY12、CY32、S31和S52携带floR,菌株CY12和CY32携带qnrD。CY32的染色体同时含有SXT/R391型整合性接合元件(integrative and conjugative elements,ICEs)(ICEPmiJpn1)和PmGRI1共2种耐药基因岛。ICEs的可变区包含2个串联的复合型转座子(IS10构成),其中一个复合型转座子携带bla_(CMY-2);CY32的PmGRI1耐药岛含有12个耐药基因。与其他奇异变形杆菌携带的PmGRI1相比,多重耐药区差异最大的区域位于Tn21转座子。此外,CY32包含2个质粒,包括携带floR的IncQ质粒和携带qnrD的非接合质粒。奇异变形杆菌CY32携带15个耐药基因,呈现多重耐药的特性。【结论】奇异变形杆菌经基因岛和质粒获得多重耐药,使治疗奇异变形杆菌感染变得更加困难,应加强对动物源奇异变形杆菌耐药性监测。展开更多
Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified ...Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.展开更多
AIM:To apply a new,integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori(H.pylori).METHODS:A genomic barcode imaging method(converting frequency matrices...AIM:To apply a new,integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori(H.pylori).METHODS:A genomic barcode imaging method(converting frequency matrices to grey-scale levels)was designed to visually distinguish origin-specific genomic regions in H.pylori.The complete genome sequences of the six H.pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned,and compared to the genome barcodes of Escherichia coli(E.coli)O157:H7 strain EDL933 and a random nucleotide sequence.The following criteria were applied to identify potential pathogenicity islands(PAIs):(1)barcode distance distinct from that of the general background;(2)length greater than 10000 continuous base pairs;and(3)containing genes with known virulence-related functions(as determined by PfamScan and Blast2GO).RESULTS:Comparison of the barcode images generated for the 26695,HPAG1,J99,Shi470,G27 and P12 H.pylori genomes with those for the E.coli and random sequence controls revealed that H.pylori genomes contained fewer anomalous regions.Among the H.pylorispecific continuous anomalous regions(longer than 20 kbp in each strain's genome),two fit the criteria for identifying candidate PAIs.The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag PAI,this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs,and characterized the other as a novel PAI,which was designated as tfs3-PAI.Furthermore,the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy.CONCLUSION:Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes,such as H.pylori,to identify candidate PAIs.展开更多
A novel technique for finding pathogenicity islands in genome data with independent component analyses(ICA) is present. First denoise the genomic signal sequences with ICA and detect G+C patterns in genomes by compari...A novel technique for finding pathogenicity islands in genome data with independent component analyses(ICA) is present. First denoise the genomic signal sequences with ICA and detect G+C patterns in genomes by comparing the result sequence with original sequences. The results on G+C patterns analysis of Dradiodurans chromosome I and N.serogroup A strain Z2491 are present. A set of loci that have very different G+C content and have not previously described are detected. The findings show that ICA is a powerful tool to detect differences within and between genomes and to separate small (gene level) and large (putative pathogenicity islands) genomic regions that have different composition characteristics.展开更多
An imported dog was confirmed to be positive with canine brucellosis in Sweden in 2010. The whole genome of Brucella canis SVA10 was subjected to phage analysis (WGS-PA) and was assigned to the Asian B. canis cluster....An imported dog was confirmed to be positive with canine brucellosis in Sweden in 2010. The whole genome of Brucella canis SVA10 was subjected to phage analysis (WGS-PA) and was assigned to the Asian B. canis cluster. Further analysis indicated that the genome of B. canis SVA10 is smaller compared to genomes of the same species. A 35,781 bp genomic island (GI) was found to be absent in strain SVA10 which was detected by read mapping the paired reads to the genome of B. canis ATCC 23,365T. The lacking genes of genomic island GIFeGSH are mainly coding for iron uptake enzymes and parts of the glutathione pathway. A screening of all available whole genome sequences of Brucella strains confirmed that GIFeGSH is also missing in four more strains of B. canis but present in several strains of B. abortus, B. melitensis, B. suis, B. ovis, B. microti, B. pinnipedialis, and B. ceti. Parts of the GI were present, but scattered in two other B. canis strains. The aim of this study was to find differences in the genomes of Brucella which might explain former described differences in virulence. The analysis was extended to all available Brucella genomes after the detection of a genomic island in strain SVA10.展开更多
基金supported by Croatian Science Foundation project IP-2018–01-8708-Application of NGS methods in the assessment of genomic variability in ruminants–“ANAGRAMS”the EU Operational Program Competitiveness and Cohesion 2014–2020 project KK.01.1.1.04.0058—Potential of microencapsulation in cheese productionthe project No.QK1919156 of the Ministry of Agriculture,Czech Republic.
文摘Background The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations.Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production(carcass,wool and milk yield).Therefore,eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation(EAS),are generally considered as multipurpose breeds(milk,meat and wool),not specialised for a particular type of production,but known for their robustness and resistance to certain environmental conditions.Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures,decipher their biological and productive functionality,and provide a"genomic"characterization of EAS adaptation and determine its production type.Results We identified positive selection signatures in EAS using several methods based on reduced local variation,linkage disequilibrium and site frequency spectrum(eROHi,iHS,nSL and CLR).Our analyses identified numerous genomic regions and genes(e.g.,desmosomal cadherin and desmoglein gene families)associated with environmental adaptation and economically important traits.Most candidate genes were related to meat/production and health/immune response traits,while some of the candidate genes discovered were important for domestication and evolutionary processes(e.g.,HOXa gene family and FSIP2).These results were also confirmed by GO and QTL enrichment analysis.Conclusions Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type,ultimately providing a new opportunity for future breeding programmes.At the same time,the numerous genes identified will improve our understanding of ruminant(sheep)robustness and resistance in the harsh and specific Mediterranean environment.
基金supported by the Guangdong Provincial Key R&D Program (2022B1111040001)the Second Tibetan Plateau Scientific Expedition and Research Program (2019QZKK0402/2019QZKK0501)National Natural Science Foundation of China (32170426)。
文摘Widespread species that inhabit diverse environments possess large population sizes and exhibit a high capacity for environmental adaptation,thus enabling range expansion.In contrast,narrow-range species are confined to restricted geographical areas and are ecologically adapted to narrow environmental conditions,thus limiting their ability to expand into novel environments.However,the genomic mechanisms underlying the differentiation between closely related species with varying distribution ranges remain poorly understood.The Niviventer niviventer species complex(NNSC),consisting of highly abundant wild rats in Southeast Asia and China,offers an excellent opportunity to investigate these questions due to the presence of both widespread and narrow-range species that are phylogenetically closely related.In the present study,we combined ecological niche modeling with phylogenetic analysis,which suggested that sister species cannot be both widespread and dominant within the same geographical region.Moreover,by assessing heterozygosity,linkage disequilibrium decay,and Tajima's D analysis,we found that widespread species exhibited higher genetic diversity than narrow-range species.In addition,by exploring the“genomic islands of speciation”,we identified 13 genes in highly divergent regions that were shared by the two widespread species,distinguishing them from their narrow-range counterparts.Functional annotation analysis indicated that these genes are involved in nervous system development and regulation.The adaptive evolution of these genes likely played an important role in the speciation of these widespread species.
文摘【目的】研究bla_(CMY-2)阳性禽源奇异变形杆菌的多重耐药特征,并分析菌株CY32全基因组序列结构。【方法】对5株bla_(CMY-2)阳性禽源奇异变形杆菌进行氟苯尼考和质粒介导氟喹诺酮类耐药基因检测、接合试验和bla_(CMY-2)基因的Southern杂交定位,对其中一株菌CY32进行全基因测序和生物信息学分析。【结果】5株奇异变形杆菌携带的bla_(CMY-2)位于染色体,其中,菌株CY12、CY32、S31和S52携带floR,菌株CY12和CY32携带qnrD。CY32的染色体同时含有SXT/R391型整合性接合元件(integrative and conjugative elements,ICEs)(ICEPmiJpn1)和PmGRI1共2种耐药基因岛。ICEs的可变区包含2个串联的复合型转座子(IS10构成),其中一个复合型转座子携带bla_(CMY-2);CY32的PmGRI1耐药岛含有12个耐药基因。与其他奇异变形杆菌携带的PmGRI1相比,多重耐药区差异最大的区域位于Tn21转座子。此外,CY32包含2个质粒,包括携带floR的IncQ质粒和携带qnrD的非接合质粒。奇异变形杆菌CY32携带15个耐药基因,呈现多重耐药的特性。【结论】奇异变形杆菌经基因岛和质粒获得多重耐药,使治疗奇异变形杆菌感染变得更加困难,应加强对动物源奇异变形杆菌耐药性监测。
基金funded by the Natural Science Foundations of China(No.31572357)to FPZAgricultural Science and Technology Innovation Program(ASTIP-IAS02)to LXW.
文摘Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.
基金Supported by Grants from the National Natural Science Foundation of China,No. 81271897 and 81071424the National Basic Research Program of China 973 Program,No. 2011CB512003+4 种基金the Specialized Research Fund for the Doctoral Program of Higher Education of China,No. 20110061120093the China Postdoctoral Science Foundation,No. 20110491311 and 2012T50285the Foundation of Xinjiang Provincial Science and Technology Department,No. 201091148the Foundation of Jilin Provincial Health Department,No. 2011Z049the Norman Bethune Program of Jilin University,No. 2012219
文摘AIM:To apply a new,integrated technique for visualizing bacterial genomes to identify novel pathogenicity islands in Helicobacter pylori(H.pylori).METHODS:A genomic barcode imaging method(converting frequency matrices to grey-scale levels)was designed to visually distinguish origin-specific genomic regions in H.pylori.The complete genome sequences of the six H.pylori strains published in the National Center for Biotechnological Information prokaryotic genome database were scanned,and compared to the genome barcodes of Escherichia coli(E.coli)O157:H7 strain EDL933 and a random nucleotide sequence.The following criteria were applied to identify potential pathogenicity islands(PAIs):(1)barcode distance distinct from that of the general background;(2)length greater than 10000 continuous base pairs;and(3)containing genes with known virulence-related functions(as determined by PfamScan and Blast2GO).RESULTS:Comparison of the barcode images generated for the 26695,HPAG1,J99,Shi470,G27 and P12 H.pylori genomes with those for the E.coli and random sequence controls revealed that H.pylori genomes contained fewer anomalous regions.Among the H.pylorispecific continuous anomalous regions(longer than 20 kbp in each strain's genome),two fit the criteria for identifying candidate PAIs.The bioinformatic-based functional analyses revealed that one of the two anomalous regions was the known pathogenicity island cag PAI,this finding also served as proof-of-principle for the utility of the genomic barcoding approach for identifying PAIs,and characterized the other as a novel PAI,which was designated as tfs3-PAI.Furthermore,the cag-PAI and tfs3-PAI harbored genes encoding type IV secretion system proteins and were predicted to have potential for functional synergy.CONCLUSION:Genomic barcode imaging represents an effective bioinformatic-based approach for scanning bacterial genomes,such as H.pylori,to identify candidate PAIs.
基金Supported by the Electronic Science Foundation of China (No.51415010101DZ02)
文摘A novel technique for finding pathogenicity islands in genome data with independent component analyses(ICA) is present. First denoise the genomic signal sequences with ICA and detect G+C patterns in genomes by comparing the result sequence with original sequences. The results on G+C patterns analysis of Dradiodurans chromosome I and N.serogroup A strain Z2491 are present. A set of loci that have very different G+C content and have not previously described are detected. The findings show that ICA is a powerful tool to detect differences within and between genomes and to separate small (gene level) and large (putative pathogenicity islands) genomic regions that have different composition characteristics.
基金supported by the Swedish Civil Contingencies Agency(MSB).
文摘An imported dog was confirmed to be positive with canine brucellosis in Sweden in 2010. The whole genome of Brucella canis SVA10 was subjected to phage analysis (WGS-PA) and was assigned to the Asian B. canis cluster. Further analysis indicated that the genome of B. canis SVA10 is smaller compared to genomes of the same species. A 35,781 bp genomic island (GI) was found to be absent in strain SVA10 which was detected by read mapping the paired reads to the genome of B. canis ATCC 23,365T. The lacking genes of genomic island GIFeGSH are mainly coding for iron uptake enzymes and parts of the glutathione pathway. A screening of all available whole genome sequences of Brucella strains confirmed that GIFeGSH is also missing in four more strains of B. canis but present in several strains of B. abortus, B. melitensis, B. suis, B. ovis, B. microti, B. pinnipedialis, and B. ceti. Parts of the GI were present, but scattered in two other B. canis strains. The aim of this study was to find differences in the genomes of Brucella which might explain former described differences in virulence. The analysis was extended to all available Brucella genomes after the detection of a genomic island in strain SVA10.
