Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly oc...Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly occurs in plants belonging to the Papilionoideae and Caesalpinioideae subfamilies(Tederso0 et al.,2018;van Velzen et al.,2019).Nodulation mechanisms in Fabaceae are well studied(Yang et al.,2022),and genomic comparisons of nodulating and non-nodulating host species can provide valuable insights into the evolutionary and genetic basis of this key process.展开更多
We determined;analyzed the Shigella flexneri serotype 5(pSF5);S.dysenteriae serotype 1(pSD1)virulence plasmid genomes.The total length of pSF5 is 136513 bp,including 165 open reading frames(ORFs).Of these ORFs,133 wer...We determined;analyzed the Shigella flexneri serotype 5(pSF5);S.dysenteriae serotype 1(pSD1)virulence plasmid genomes.The total length of pSF5 is 136513 bp,including 165 open reading frames(ORFs).Of these ORFs,133 were identified;32 of those had no significant homology to proteins with known functions.The length of pSD1 is 182545 bp,including 224 ORFs,of which we identified 181.The remaining 43 ORFs were not significantly homologous to proteins with known functions.The insertion sequence(IS)elements are 53787 bp in pSF5,;49616 bp in pSD1,which represents 39.4%;27.1%of the genome,respectively.There are 22 IS element types in pSF5;pSD1,among which we report ISEc8;ISSbo6 for the first time in the Shigella virulence plasmid.Compared to pCP301,there are a large number of deleted genes;gene inversions in both pSF5;pSD1.The ipa-mxi-spa locus in pSF5 is completely absent,;the genes related to the O-antigen biosynthesis are partially missing.In contrast,the above genes in pSD1 are integral,with the exception of virF.The whole genome analysis of the two plasmids shows that the loss of genes related to gene invasion or regulation also obliterates the ability of pPF5;pSD1 to bind Congo red(Crb).Whether these genes determine the Crb function requires continued investigation.展开更多
The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences c...The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/and https://github.com/wushyer/RGAAT;2 at no cost.展开更多
Vibrio parahaemolyticus is a marine bacterium and a causative agent of gastroenteritis in humans.Phages targeting V.parahaemolyticus serve as natural antagonists to this pathogen,significantly controlling its populati...Vibrio parahaemolyticus is a marine bacterium and a causative agent of gastroenteritis in humans.Phages targeting V.parahaemolyticus serve as natural antagonists to this pathogen,significantly controlling its population and,consequently,disease outbreaks.In this study,two myoviruses,vB_VpaM_R20L(R20L)and vB_VpaM_R19R(R19R),were isolated and characterized against V.parahaemolyticus ATCC 17802 T.Despite their genomic resemblance,phages R19R and R20L displayed notable differences in physiological characteristics,particularly in infection dynamics and thermal stability.Both phages had a latent period of approximately 10 min;however,R19R demonstrated significantly greater replication efficiency,with a burst size of 388 PFU/cell compared to 90 PFU/cell for R20L.Thermal stability assays showed that R20L maintained survival rates of 80%–100%at 5℃–45℃ for over three days,while R19R’s viability declined to 50%within 12 h under the same conditions.Furthermore,molecular dynamics simulations identified the influence of temperature on the thermal stability of phages,primarily through impact on the structural proteins.These findings suggest that subtle genomic variations may drive differences in physiological characteristics,highlighting the complexity of vibriophage-host interactions and their selection in response to natural environmental pressures.展开更多
The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and...The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and to explore potential resistance mechanisms,56 MRAB strains were collected from the clinical departments of seven hospitals in Liaocheng between 2020 and 2022.Molecular typing,antimicrobial resistance patterns,and epidemiological characteristics were determined by genome sequencing and comparative genome analysis.Sequence type(ST)540 was the most prevalent ST of the 56 MRAB in Liaocheng,and most strains(92.86%)were grouped into CC92.Core genome multilocus sequence typing subdivided the strains according to the number of allelic differences and could distinguish different outbreaks caused by ST540 isolates in the hospitals.All the isolates harbored blaOXA-23 and blaADC-25,and at least 92.86%of the isolates were resistant to 10 antibiotics.The major MRAB epidemic clone detected in Liaocheng was ST540,which was different from the results reported in other regions in China.Furthermore,several inter-hospital transmissions of ST540 isolates were observed.The findings highlight the urgent need for effective nosocomial infection control measures and the continuous surveillance of ST540 MRAB in Liaocheng.展开更多
基金supported by the National Natural Science Foundation of China(No.32160142)Guangxi Natural Science Foundation(No.2023GXNSFDA026034)+3 种基金State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources(SKLCUSAb202302)to H.W.,the National Natural Science Foundation of China(No.32460062)to Y.L.,and 1+9 Leading the Charge with Open Competition'project of Sichuan Academy of Agricultural Sciences(1+9KJGG010)Fruit tree breeding project in Sichuan Province(2021YFYZ0023)to H.X.
文摘Symbiotic nitrogen fixation in members of the Fabaceae family is highly efficient and beneficial for global agriculture,but not all species in this family form root nodules with rhizobial bacteria.Nodulation mainly occurs in plants belonging to the Papilionoideae and Caesalpinioideae subfamilies(Tederso0 et al.,2018;van Velzen et al.,2019).Nodulation mechanisms in Fabaceae are well studied(Yang et al.,2022),and genomic comparisons of nodulating and non-nodulating host species can provide valuable insights into the evolutionary and genetic basis of this key process.
基金supported by the State Key Basic Research Program(Grant No.2005CB522904)the High Technology Project(Grant No.2001AA223011)+1 种基金Interational Science and Technology Co-operation Project(Grant No.2001AA223116)Beijing Science and Tech-nology Project(Contract No.H010210360119).
文摘We determined;analyzed the Shigella flexneri serotype 5(pSF5);S.dysenteriae serotype 1(pSD1)virulence plasmid genomes.The total length of pSF5 is 136513 bp,including 165 open reading frames(ORFs).Of these ORFs,133 were identified;32 of those had no significant homology to proteins with known functions.The length of pSD1 is 182545 bp,including 224 ORFs,of which we identified 181.The remaining 43 ORFs were not significantly homologous to proteins with known functions.The insertion sequence(IS)elements are 53787 bp in pSF5,;49616 bp in pSD1,which represents 39.4%;27.1%of the genome,respectively.There are 22 IS element types in pSF5;pSD1,among which we report ISEc8;ISSbo6 for the first time in the Shigella virulence plasmid.Compared to pCP301,there are a large number of deleted genes;gene inversions in both pSF5;pSD1.The ipa-mxi-spa locus in pSF5 is completely absent,;the genes related to the O-antigen biosynthesis are partially missing.In contrast,the above genes in pSD1 are integral,with the exception of virF.The whole genome analysis of the two plasmids shows that the loss of genes related to gene invasion or regulation also obliterates the ability of pPF5;pSD1 to bind Congo red(Crb).Whether these genes determine the Crb function requires continued investigation.
基金supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (Grant No. XDA08020102)National Natural Science Foundation of China (Grant Nos. 81701071, 31501042, 31271385, and 31200957)+2 种基金Shenzhen Science and Technology Program (Grant No. JCYJ20170306171013613),ChinaKing Abdulaziz City for Science and Technology (KACSTGrant No. 1035-35),Kingdom of Saudi Arabia
文摘The rapid development of high-throughput sequencing technologies has led to a dramatic decrease in the money and time required for de novo genome sequencing or genome resequencing projects, with new genome sequences constantly released every week. Among such projects, the plethora of updated genome assemblies induces the requirement of versiondependent annotation files and other compatible public dataset for downstream analysis. To handlethese tasks in an efficient manner, we developed the reference-based genome assembly and annotation tool（RGAAT）, a flexible toolkit for resequencing-based consensus building and annotation update. RGAAT can detect sequence variants with comparable precision, specificity, and sensitivity to GATK and with higher precision and specificity than Freebayes and SAMtools on four DNAseq datasets tested in this study. RGAAT can also identify sequence variants based on cross-cultivar or cross-version genomic alignments. Unlike GATK and SAMtools/BCFtools, RGAAT builds the consensus sequence by taking into account the true allele frequency. Finally, RGAAT generates a coordinate conversion file between the reference and query genomes using sequence variants and supports annotation file transfer. Compared to the rapid annotation transfer tool（RATT）,RGAAT displays better performance characteristics for annotation transfer between different genome assemblies, strains, and species. In addition, RGAAT can be used for genome modification,genome comparison, and coordinate conversion. RGAAT is available at https://sourceforge.net/projects/rgaat/and https://github.com/wushyer/RGAAT;2 at no cost.
基金supported by the Guangdong Major Project of Basic and Applied Basic Research(2023B0303000017)the National Natural Science Foundation of China(42188102,42106194)+2 种基金the Innovation Team Project of Universities in Guangdong Province(No.2023KCXTD028)the Science and Technology Development Fund,Macao SAR(File/Project no.0055.2023.RIB2)the research fund from Synthetic Biology Research Center of Shenzhen University.
文摘Vibrio parahaemolyticus is a marine bacterium and a causative agent of gastroenteritis in humans.Phages targeting V.parahaemolyticus serve as natural antagonists to this pathogen,significantly controlling its population and,consequently,disease outbreaks.In this study,two myoviruses,vB_VpaM_R20L(R20L)and vB_VpaM_R19R(R19R),were isolated and characterized against V.parahaemolyticus ATCC 17802 T.Despite their genomic resemblance,phages R19R and R20L displayed notable differences in physiological characteristics,particularly in infection dynamics and thermal stability.Both phages had a latent period of approximately 10 min;however,R19R demonstrated significantly greater replication efficiency,with a burst size of 388 PFU/cell compared to 90 PFU/cell for R20L.Thermal stability assays showed that R20L maintained survival rates of 80%–100%at 5℃–45℃ for over three days,while R19R’s viability declined to 50%within 12 h under the same conditions.Furthermore,molecular dynamics simulations identified the influence of temperature on the thermal stability of phages,primarily through impact on the structural proteins.These findings suggest that subtle genomic variations may drive differences in physiological characteristics,highlighting the complexity of vibriophage-host interactions and their selection in response to natural environmental pressures.
基金funded by the Shandong Medical and Health Science and Technology Development Program,grant number 202212061076.
文摘The emergence and prevalence of multidrug-resistant Acinetobacter baumannii(MRAB)poses a huge challenge to clinical treatment.To investigate the genetic and epidemiologic characteristics of MRAB in Liaocheng,China,and to explore potential resistance mechanisms,56 MRAB strains were collected from the clinical departments of seven hospitals in Liaocheng between 2020 and 2022.Molecular typing,antimicrobial resistance patterns,and epidemiological characteristics were determined by genome sequencing and comparative genome analysis.Sequence type(ST)540 was the most prevalent ST of the 56 MRAB in Liaocheng,and most strains(92.86%)were grouped into CC92.Core genome multilocus sequence typing subdivided the strains according to the number of allelic differences and could distinguish different outbreaks caused by ST540 isolates in the hospitals.All the isolates harbored blaOXA-23 and blaADC-25,and at least 92.86%of the isolates were resistant to 10 antibiotics.The major MRAB epidemic clone detected in Liaocheng was ST540,which was different from the results reported in other regions in China.Furthermore,several inter-hospital transmissions of ST540 isolates were observed.The findings highlight the urgent need for effective nosocomial infection control measures and the continuous surveillance of ST540 MRAB in Liaocheng.
