Prospects for Comparative Genome Analyses Among Mammals

1996 ◽  
pp. 115-125
Author(s):  
Leslie A. Lyons ◽  
Stephen J. O’Brien
Keyword(s):  
Comparative Genome ◽  
Genome Analyses

Comparative genome analyses of novel Mangrovimonas -like strains isolated from estuarine mangrove sediments reveal xylan and arabinan utilization genes

2016 ◽  
Vol 25 ◽  
pp. 115-121 ◽  
Author(s):  
Balachandra Dinesh ◽  
Nyok-Sean Lau ◽  
Go Furusawa ◽  
Seok-Won Kim ◽  
Todd D. Taylor ◽  
...  
Keyword(s):  
Mangrove Sediments ◽  
Comparative Genome ◽  
Genome Analyses

scholarly journals Whole genome sequence and comparative genome analyses of multi-resistant Staphylococcus warneri GD01 isolated from a diseased pig in China

PLoS ONE ◽  
2020 ◽  
Vol 15 (5) ◽  
pp. e0233363
Author(s):  
Canying Liu ◽  
Xianjie Zhao ◽  
Honglin Xie ◽  
Xi Zhang ◽  
Kangjian Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Comparative Genome ◽  
Staphylococcus Warneri ◽  
Genome Analyses

scholarly journals Comparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits

mSystems ◽  
2017 ◽  
Vol 2 (1) ◽  
Author(s):  
Daniel Castillo ◽  
Paul D. Alvise ◽  
Ruiqi Xu ◽  
Faxing Zhang ◽  
Mathias Middelboe ◽  
...  
Keyword(s):  
Virulence Factors ◽  
Bacterial Species ◽  
Vibrio Anguillarum ◽  
Genomic Diversity ◽  
Comparative Genome ◽  
Accessory Genome ◽  
Pan Genome ◽  
Virulent Strains ◽  
Genome Analyses ◽  
Unique Core

ABSTRACT Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes. Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity. Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.

scholarly journals Comparative Genome Analyses of Serratia marcescens FS14 Reveals Its High Antagonistic Potential

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0123061 ◽  
Author(s):  
Pengpeng Li ◽  
Amy H. Y. Kwok ◽  
Jingwei Jiang ◽  
Tingting Ran ◽  
Dongqing Xu ◽  
...  
Keyword(s):  
Serratia Marcescens ◽  
Comparative Genome ◽  
Antagonistic Potential ◽  
Genome Analyses

scholarly journals Development of a Rhizoctonia solani AG1-IB Specific Gene Model Enables Comparative Genome Analyses between Phytopathogenic R. solani AG1-IA, AG1-IB, AG3 and AG8 Isolates

PLoS ONE ◽  
2015 ◽  
Vol 10 (12) ◽  
pp. e0144769 ◽  
Author(s):  
Daniel Wibberg ◽  
Oliver Rupp ◽  
Jochen Blom ◽  
Lukas Jelonek ◽  
Magdalena Kröber ◽  
...  
Keyword(s):  
Rhizoctonia Solani ◽  
Specific Gene ◽  
Gene Model ◽  
Comparative Genome ◽  
Genome Analyses

scholarly journals Comparative Genome Analyses Reveal the Genomic Traits and Host Plant Adaptations of Flavobacterium akiainvivens IK-1T

2019 ◽  
Vol 20 (19) ◽  
pp. 4910
Author(s):  
Xuehua Wan
Keyword(s):  
Plant Interactions ◽  
Secretion Systems ◽  
Two Component System ◽  
Gene Expressions ◽  
Plant Host ◽  
Comparative Genome ◽  
Plant Adaptations ◽  
Factor Type ◽  
Genome Analyses ◽  
Von Willebrand

The genus Flavobacterium contains a large group of commensal bacteria identified in diverse terrestrial and aquatic habitats. We compared the genome of a new species Flavobacterium akiainvivens IK-1T to public available genomes of Flavobacterium species to reveal the genomic traits and ecological roles of IK-1T. Principle component analysis (PCA) of carbohydrate-active enzyme classes suggests that IK-1T belongs to a terrestrial clade of Flavobacterium. In addition, type 2 and type 9 secretion systems involved in bacteria-environment interactions were identified in the IK-1T genome. The IK-1T genome encodes eukaryotic-like domain containing proteins including ankyrin repeats, von Willebrand factor type A domain, and major royal jelly proteins, suggesting that IK-1T may alter plant host physiology by secreting eukaryotic-like proteins that mimic host proteins. A novel two-component system FaRpfC-FaYpdB was identified in the IK-1T genome, which may mediate quorum sensing to regulate global gene expressions. Our findings suggest that comparative genome analyses of Flavobacterium spp. reveal that IK-1T has adapted to a terrestrial niche. Further functional characterizations of IK-1T secreted proteins and their regulation systems will shed light on molecular basis of bacteria-plant interactions in environments.

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