scholarly journals APPLICATION OF COMPARATIVE GENOME IN AQUACULTURE DISEASES DIAGNOSIS

2020 ◽  
Vol 1 (40) ◽  
pp. 172-179
Author(s):  
Luan Thanh Nguyen
Keyword(s):  
Genome Analysis ◽  
Pathogenic Bacteria ◽  
Control Method ◽  
Bacterial Pathogen ◽  
Pathogen Transmission ◽  
Aquatic Animal ◽  
Comparative Genome ◽  
Global Food Security ◽  
Pan Genome ◽  
Aquatic Pathogens

The sustainability of aquaculture industry is critical both for global food security and economic welfare. However, the massive wealth of pathogenic bacteria poses a key challenge to the development of a sustainable bio-control method. Recent advances in genome sequencing study combined  with pan-genome analysis can be an efficacious management applied to numerous aquatic pathogens. Thus, routine comparative genome analyses of aquatic pathogens will deduce the phylogenomic diversity and possible evolutionary trendsof aquatic bacterial pathogen strains, elucidate the mechanisms of pathogenesis, as well as estimate patterns of pathogen transmission across epidemiological scales. This study also reviews comparative pan-genome analysis with a particular focus on controlling aquatic diseases, especially for: (i) re-identifying the previously misidentified strain with high accuracy and discovering novel isolates that may be associated with high rateof fish mortalities, (ii) developing routine pan-PCR based on highly informative identified genetic targets that are capable of distinguishing all the clinical isolates, and finally (iii) studying the multivalent vaccine following reverse vaccinology towards the prevention of numerous aquatic animal diseases.

scholarly journals GENOME COMPARATIVE OF EDWARDSIELLA REVEALS POTENTIAL DEVELOPMENT OF SUSTAINABLE PROPHYLAXES

2020 ◽  
Vol 1 (1) ◽  
pp. 23-25
Author(s):  
Nguyen Thanh Luan
Keyword(s):  
Genome Analysis ◽  
Pathogenic Bacteria ◽  
Control Method ◽  
In Silico Analysis ◽  
Core Gene ◽  
Farmed Fish ◽  
Gene Encoding ◽  
Pan Genome ◽  
Adhesion Ability ◽  
Potential Development

Aquatic diseases caused by the massive wealth of pathogenic bacteria pose major challenges to the development of a sustainable bio-control method, such as antimicrobial measures and vaccine strategies. Recent advances in genome sequencing technology have revolutionized the field of pathogenic pan-genomics and have also influenced disease management in aqua farms. In this study, Edwardsiella strains were differentially classified into four species by a phylogenomics construction based on the pan-genome analysis. Edwardsiella species were correctly classified by pan-genome analysis (core gene, dispensable gene, singleton gene) of 15 complete genomes. Based on the presence of the gene repertoires, gene encoding extracellular protein, outer membrane protein, adhesion ability and antigenic sites, 9 genes (E. ictaluri), 13 genes (E. anguilarium), 9 genes (E. piscicida), 12 genes (E. tadar), and 14 genes (all species) screened from core-gene of 2686, 2673, 2877, 2920, and 1957 gene, respectively have potential in developing reverse vaccinology strategy to the prevention of Edwarsiellosis. The in-silico analysis will also help to optimize the time and improve the cross-serotype reaction of vaccines in farmed fish. The RV research implementing pan-genome analysis will be a strategy that is applicable to pathogens in both aquatic and terrestrial animals.

Current status of pan-genome analysis for pathogenic bacteria

2020 ◽  
Vol 63 ◽  
pp. 54-62 ◽  
Author(s):  
Yeji Kim ◽  
Changdai Gu ◽  
Hyun Uk Kim ◽  
Sang Yup Lee
Keyword(s):  
Genome Analysis ◽  
Pathogenic Bacteria ◽  
Current Status ◽  
Pan Genome

scholarly journals Genome-wide comparison of four MRSA clinical isolates from Germany and Hungary

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e10185
Author(s):  
Romen Singh Naorem ◽  
Jochen Blom ◽  
Csaba Fekete
Keyword(s):  
Genome Analysis ◽  
Genetic Background ◽  
Multiple Drug Resistance ◽  
Clinical Isolates ◽  
Ecological Niches ◽  
Comparative Genome Analysis ◽  
Pathogenic Potential ◽  
Comparative Genome ◽  
Pan Genome ◽  
Niche Adaptation

Staphylococcus aureus is a drug-resistant pathogen, capable of colonizing diverse ecological niches and causing a broad spectrum of infections related to a community and healthcare. In this study, we choose four methicillin-resistant S. aureus (MRSA) clinical isolates from Germany and Hungary based on our previous polyphasic characterization finding. We assumed that the selected strains have a different genetic background in terms of the presence of resistance and virulence genes, prophages, plasmids, and secondary metabolite biosynthesis genes that may play a crucial role in niche adaptation and pathogenesis. To clarify these assumptions, we performed a comparative genome analysis of these strains and observed many differences in their genomic compositions. The Hungarian isolates (SA H27 and SA H32) with ST22-SCCmec type IVa have fewer genes for multiple-drug resistance, virulence, and prophages reported in Germany isolates. Germany isolate, SA G6 acquires aminoglycoside (ant(6)-Ia and aph(3’)-III) and nucleoside (sat-4) resistance genes via phage transduction and may determine its pathogenic potential. The comparative genome study allowed the segregation of isolates of geographical origin and differentiation of the clinical isolates from the commensal isolates. This study suggested that Germany and Hungarian isolates are genetically diverse and showing variation among them due to the gain or loss of mobile genetic elements (MGEs). An interesting finding is the addition of SA G6 genome responsible for the drastic decline of the core/pan-genome ratio curve and causing the pan-genome to open wider. Functional characterizations revealed that S. aureus isolates survival are maintained by the amino acids catabolism and favor adaptation to growing in a protein-rich medium. The dispersible and singleton genes content of S. aureus genomes allows us to understand the genetic variation among the CC5 and CC22 groups. The strains with the same genetic background were clustered together, which suggests that these strains are highly alike; however, comparative genome analysis exposed that the acquisition of phage elements, and plasmids through the events of MGEs transfer contribute to differences in their phenotypic characters. This comparative genome analysis would improve the knowledge about the pathogenic S. aureus strain’s characterization, and responsible for clinically important phenotypic differences among the S. aureus strains.

scholarly journals Comparative genomics of Klebsiella michiganensis BD177 and related members of Klebsiella sp. reveal the symbiotic relationship with Bactrocera dorsalis

BMC Genetics ◽  
2020 ◽  
Vol 21 (S2) ◽  
Author(s):  
Zhaohui Cai ◽  
Qiongyu Guo ◽  
Zhichao Yao ◽  
Wenping Zheng ◽  
Junfei Xie ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Complete Genome ◽  
Type Strain ◽  
Bactrocera Dorsalis ◽  
Symbiotic Relationship ◽  
Comparative Genome Analysis ◽  
Circular Chromosome ◽  
Comparative Genome ◽  
Ecological Fitness ◽  
Pan Genome

Abstract Background Bactrocera dorsalis is a destructive polyphagous and highly invasive insect pest of tropical and subtropical species of fruit and vegetable crops. The sterile insect technique (SIT) has been used for decades to control insect pests of agricultural, veterinary, and human health importance. Irradiation of pupae in SIT can reduce the ecological fitness of the sterile insects. Our previous study has shown that a gut bacterial strain BD177 that could restore ecological fitness by promoting host food intake and metabolic activities. Results Using long-read sequence technologies, we assembled the complete genome of K. michiganensis BD177 strain. The complete genome of K. michiganensis BD177 comprises one circular chromosome and four plasmids with a GC content of 55.03%. The pan-genome analysis was performed on 119 genomes (strain BD177 genome and 118 out of 128 published Klebsiella sp. genomes since ten were discarded). The pan-genome includes a total of 49305 gene clusters, a small number of 858 core genes, and a high number of accessory (10566) genes. Pan-genome and average nucleotide identity (ANI) analysis showed that BD177 is more similar to the type strain K. michiganensis DSM2544, while away from the type strain K. oxytoca ATCC13182. Comparative genome analysis with 21 K. oxytoca and 12 K. michiganensis strains, identified 213 unique genes, several of them related to amino acid metabolism, metabolism of cofactors and vitamins, and xenobiotics biodegradation and metabolism in BD177 genome. Conclusions Phylogenomics analysis reclassified strain BD177 as a member of the species K. michiganensis. Comparative genome analysis suggested that K. michiganensis BD177 has the strain-specific ability to provide three essential amino acids (phenylalanine, tryptophan and methionine) and two vitamins B (folate and riboflavin) to B. dorsalis. The clear classification status of BD177 strain and identification of unique genetic characteristics may contribute to expanding our understanding of the symbiotic relationship of gut microbiota and B. dorsalis.

Synteny Conservation and Chromosome Rearrangements During Mammalian Evolution

Genetics ◽  
1997 ◽  
Vol 147 (1) ◽  
pp. 289-296 ◽  
Author(s):  
Jason Ehrlich ◽  
David Sankoff ◽  
Joseph H Nadeau
Keyword(s):  
Genome Analysis ◽  
Systematic Errors ◽  
Chromosome Rearrangements ◽  
Mammalian Evolution ◽  
Comparative Genome Analysis ◽  
Reciprocal Translocations ◽  
Comparative Genome ◽  
Strong Selection ◽  
Synteny Conservation

Abstract An important problem in comparative genome analysis has been defining reliable measures of synteny conservation. The published analytical measures of synteny conservation have limitations. Nonindependence of comparisons, conserved and disrupted syntenies that are as yet unidentified, and redundant rearrangements lead to systematic errors that tend to overestimate the degree of conservation. We recently derived methods to estimate the total number of conserved syntenies within the genome, counting both those that have already been described and those that remain to be discovered. With this method, we show that ~65% of the conserved syntenies have already been identified for humans and mice, that rates of synteny disruption vary ~25-fold among mammalian lineages, and that despite strong selection against reciprocal translocations, inter-chromosome rearrangements occurred approximately fourfold more often than inversions and other intra-chromosome rearrangements, at least for lineages leading to humans and mice.

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