scholarly journals Genomic Analysis of Wolbachia from Laodelphax striatellus (Delphacidae, Hemiptera) Reveals Insights into Its “Jekyll and Hyde” Mode of Infection Pattern

2020 ◽  
Vol 12 (2) ◽  
pp. 3818-3831 ◽  
Author(s):  
Xiao-Li Bing ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
Kai-Jun Zhang ◽  
Xiao-Yue Hong
Keyword(s):  
Draft Genome ◽  
Genomic Analysis ◽  
Phylogenomic Analysis ◽  
Laodelphax Striatellus ◽  
Secretion Systems ◽  
Negative Effects ◽  
Protein Coding ◽  
Catalytic Domains ◽  
Infection Pattern ◽  
Wolbachia Genome

Abstract Wolbachia is a widely distributed intracellular bacterial endosymbiont among invertebrates. The wStriCN, the Wolbachia strain that naturally infects an agricultural pest Laodelphax striatellus, has a “Jekyll and Hyde” mode of infection pattern with positive and negative effects: It not only kills many offspring by inducing cytoplasmic incompatibility (CI) but also significantly increases host fecundity. In this study, we assembled the draft genome of wStriCN and compared it with other Wolbachia genomes to look for clues to its Jekyll and Hyde characteristics. The assembled wStriCN draft genome is 1.79 Mb in size, which is the largest Wolbachia genome in supergroup B. Phylogenomic analysis showed that wStriCN is closest to Wolbachia from Asian citrus psyllid Diaphorina citri. These strains formed a monophylogentic clade within supergroup B. Compared with other Wolbachia genomes, wStriCN contains the most diverse insertion sequence families, the largest amount of prophage sequences, and the most ankyrin domain protein coding genes. The wStriCN genome encodes components of multiple secretion systems, including Types I, II, IV, VI, Sec, and Tac. We detected three pairs of homologs for CI factors CifA and CifB. These proteins harbor the catalytic domains responsible for CI phenotypes but are phylogenetically and structurally distinct from all known Cif proteins. The genome retains pathways for synthesizing biotin and riboflavin, which may explain the beneficial roles of wStriCN in its host planthoppers, which feed on nutrient-poor plant sap. Altogether, the genomic sequencing of wStriCN provides insight into understanding the phylogeny and biology of Wolbachia.

scholarly journals Phylogenomic analysis shows that Bacillus amyloliquefaciens subsp. plantarum is a later heterotypic synonym of Bacillus methylotrophicus

2015 ◽  
Vol 65 (Pt_7) ◽  
pp. 2104-2109 ◽  
Author(s):  
Christopher A. Dunlap ◽  
Soo-Jin Kim ◽  
Soon-Wo Kwon ◽  
Alejandro P. Rooney
Keyword(s):  
Bacillus Amyloliquefaciens ◽  
Type Strain ◽  
Plant Pathogens ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Growth Promoters ◽  
Bacillus Methylotrophicus

The rhizosphere-isolated bacteria belonging to the Bacillus amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus clades are an important group of strains that are used as plant growth promoters and antagonists of plant pathogens. These properties have made these strains the focus of commercial interest. Here, we present the draft genome sequence of B. methylotrophicus KACC 13105T ( = CBMB205T). Comparative genomic analysis showed only minor differences between this strain and the genome of the B. amyloliquefaciens subsp. plantarum type strain, with the genomes sharing approximately 95 % of the same genes. The results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar. In fact, our results show that the type strain of B. amyloliquefaciens subsp. plantarum FZB42T ( = DSM 23117T = BGSC 10A6T) does not cluster with other members of the B. amyloliquefaciens taxon. Instead, it clusters well within a clade of strains that are assigned to B. methylotrophicus, including the type strain of that species. Therefore, we propose that the subspecies B. amyloliquefaciens subsp. plantarum should be reclassified as a later heterotypic synonym of B. methylotrophicus.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Draft Genome Sequence of Anoxybacillus mongoliensis Strain MB4, a Sulfur-Utilizing Aerobic Thermophile Isolated from a Hot Spring in Tattapani, Central India

2017 ◽  
Vol 5 (9) ◽  
Author(s):  
Parul Mittal ◽  
Rituja Saxena ◽  
Vineet K. Sharma
Keyword(s):  
Genome Sequence ◽  
Hot Spring ◽  
Sulfur Metabolism ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Central India ◽  
Draft Genome Sequence ◽  
Protein Coding ◽  
Content Type ◽  
Protein Coding Genes

ABSTRACT Anoxybacillus mongoliensis strain MB4, an aerobic thermophile, was isolated from a hot spring located in central India. Its first draft genome sequence reported in this study comprises 2,807,516 bp and 2,853 protein-coding genes. Detailed genomic analysis indicates that it is capable of performing sulfur metabolism.

scholarly journals Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

2016 ◽  
Vol 2 (8) ◽  
pp. e1600633 ◽  
Author(s):  
Victor C. Mason ◽  
Gang Li ◽  
Patrick Minx ◽  
Jürgen Schmitz ◽  
Gennady Churakov ◽  
...  
Keyword(s):  
Sequence Data ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Sister Group ◽  
Phylogenomic Analysis ◽  
Isolated Populations ◽  
Conservation Units ◽  
Genetic Changes ◽  
Genomic Changes ◽  
Rare Genomic Changes

Colugos are among the most poorly studied mammals despite their centrality to resolving supraordinal primate relationships. Two described species of these gliding mammals are the sole living members of the order Dermoptera, distributed throughout Southeast Asia. We generated a draft genome sequence for a Sunda colugo and a Philippine colugo reference alignment, and used these to identify colugo-specific genetic changes that were enriched in sensory and musculoskeletal-related genes that likely underlie their nocturnal and gliding adaptations. Phylogenomic analysis and catalogs of rare genomic changes overwhelmingly support the contested hypothesis that colugos are the sister group to primates (Primatomorpha), to the exclusion of treeshrews. We captured ~140 kb of orthologous sequence data from colugo museum specimens sampled across their range and identified large genetic differences between many geographically isolated populations that may result in a >300% increase in the number of recognized colugo species. Our results identify conservation units to mitigate future losses of this enigmatic mammalian order.

scholarly journals Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

2015 ◽  
Vol 65 (Pt_10) ◽  
pp. 3507-3510 ◽  
Author(s):  
Christopher A. Dunlap
Keyword(s):  
Dna Hybridization ◽  
Core Genome ◽  
Phylogenetic Analyses ◽  
Draft Genome ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
Phylogenomic Analysis ◽  
Sequencing Analysis ◽  
Emended Description ◽  
Type Strains

‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
Chengqian Qian ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Cationic Antimicrobial Peptide ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Genome sequence of the wheat stem sawfly, Cephus cinctus, a primitive hymenopteran and wheat pest, illuminates evolution of hymenopteran chemoreceptors

2018 ◽  
Author(s):  
Hugh M. Robertson ◽  
Robert M. Waterhouse ◽  
Kimberly K. O. Walden ◽  
Livio Ruzzante ◽  
Maarten J. M. F. Reijnders ◽  
...  
Keyword(s):  
Gene Family ◽  
Gene Annotation ◽  
Draft Genome ◽  
Phylogenomic Analysis ◽  
Gene Repertoire ◽  
Protein Coding ◽  
Wheat Stem Sawfly ◽  
Cephus Cinctus ◽  
Draft Genome Assembly ◽  
New Perspective

AbstractThe wheat stem sawfly, Cephus cinctus, is a major pest of wheat and key ecological player in the grasslands of western North America. It also represents a distinctive lineage of sawflies that appeared early during the hymenopteran radiation, but after the clade of Eusymphyta sawflies that is the sister lineage of all other Hymenoptera. We present a high-quality draft genome assembly of 162 Mbp in 1,976 scaffolds with a scaffold N50 of 622 kbp. Automated gene annotation identified 11,210 protein-coding gene models and 1,307 non-coding RNA models. Thirteen percent of the assembly consists of ~58,000 transposable elements partitioned equally between Class-I and Class-II elements. Orthology analysis reveals that 86% of Cephus proteins have identifiable orthologs in other insects. Phylogenomic analysis of conserved subsets of these proteins supports the placement of the Cephidae between the Eusymphyta and the parasitic woodwasp superfamily Orussoidea. Manual annotation and phylogenetic analysis of families of odorant, gustatory, and ionotropic receptors, plus odorant binding proteins, shows that Cephus has representatives for most conserved and expanded gene lineages in the Apocrita (wasps, ants, and bees). Cephus has also maintained several insect gene lineages that have been lost from the Apocrita, most prominently the carbon dioxide receptor subfamily. Furthermore, Cephus encodes a few small lineage-specific chemoreceptor gene family expansions that might be involved in adaptations to new grasses including wheat. These comparative analyses identify gene family members likely to have been present in the hymenopteran ancestor and provide a new perspective on the evolution of the chemosensory gene repertoire.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

scholarly journals Comparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity

2019 ◽  
Author(s):  
Liu Bin ◽  
Zhiqiu Yin ◽  
Chao Yuan ◽  
Yuhui Du ◽  
Pan Yang ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Resistance Genes ◽  
Efflux Pump ◽  
Draft Genome ◽  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Secretion Systems ◽  
Species Specific

Abstract Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei. Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

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