Comparative Genomics Analysis of Streptomyces Species Reveals Their Adaptation to the Marine Environment and Their Diversity at the Genomic Level

Phytopathogenic Ascomycota are responsible for substantial economic losses each year, destroying valuable crops. The present study aims to provide new insights into phytopathogenicity in Ascomycota from a comparative genomic perspective. This has been achieved by categorizing orthologous gene groups (orthogroups) from 68 phytopathogenic and 24 non-phytopathogenic Ascomycota genomes into three classes: Core, (pathogen or non-pathogen) group-specific, and genome-specific accessory orthogroups. We found that (i) ~20% orthogroups are group-specific and accessory in the 92 Ascomycota genomes, (ii) phytopathogenicity is not phylogenetically determined, (iii) group-specific orthogroups have more enriched functional terms than accessory orthogroups and this trend is particularly evident in phytopathogenic fungi, (iv) secreted proteins with signal peptides and horizontal gene transfers (HGTs) are the two functional terms that show the highest occurrence and significance in group-specific orthogroups, (v) a number of other functional terms are also identified to have higher significance and occurrence in group-specific orthogroups. Overall, our comparative genomics analysis determined positive enrichment existing between orthogroup classes and revealed a prediction of what genomic characteristics make an Ascomycete phytopathogenic. We conclude that genes shared by multiple phytopathogenic genomes are more important for phytopathogenicity than those that are unique in each genome.

Download Full-text

Comparative genomics analysis to differentiate metabolic and virulence gene potential in gastric versus enterohepatic Helicobacter species

BMC Genomics ◽

10.1186/s12864-018-5171-2 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 6

Author(s):

Anthony Mannion ◽

Zeli Shen ◽

James G. Fox

Keyword(s):

Comparative Genomics ◽

Virulence Gene ◽

Comparative Genomics Analysis

Download Full-text

Phylogenetic relationships of ascomycetes and basidiomycetes based on comparative genomics analysis

Genes & Genomics ◽

10.1007/s13258-017-0595-7 ◽

2017 ◽

Vol 39 (12) ◽

pp. 1307-1316 ◽

Cited By ~ 3

Author(s):

Xunbiao Liu ◽

Qianqian Zhang ◽

Xinyao Xia ◽

Xiuyuan Liu ◽

Lei Ge ◽

...

Keyword(s):

Comparative Genomics ◽

Phylogenetic Relationships ◽

Comparative Genomics Analysis

Download Full-text

Comparative genomics analysis of five families of antimicrobial peptide-like genes in seven ant species

Developmental & Comparative Immunology ◽

10.1016/j.dci.2012.05.003 ◽

2012 ◽

Vol 38 (2) ◽

pp. 262-274 ◽

Cited By ~ 39

Author(s):

Zhenting Zhang ◽

Shunyi Zhu

Keyword(s):

Comparative Genomics ◽

Antimicrobial Peptide ◽

Comparative Genomics Analysis

Download Full-text

Comparative Genomics Analysis of Two Different Virulent Bovine Pasteurella multocida Isolates

International Journal of Genomics ◽

10.1155/2016/4512493 ◽

2016 ◽

Vol 2016 ◽

pp. 1-14 ◽

Cited By ~ 9

Author(s):

Huihui Du ◽

Rendong Fang ◽

Tingting Pan ◽

Tian Li ◽

Nengzhang Li ◽

...

Keyword(s):

Comparative Genomics ◽

Genome Sequence ◽

Pasteurella Multocida ◽

Draft Genome ◽

Draft Genome Sequence ◽

Insertion Sequences ◽

Capsular Type ◽

Protein Coding ◽

Protein Coding Genes ◽

Comparative Genomics Analysis

The Pasteurella multocida capsular type A isolates can cause pneumonia and bovine respiratory disease (BRD). In this study, comparative genomics analysis was carried out to identify the virulence genes in two different virulent P. multocida capsular type A isolates (high virulent PmCQ2 and low virulent PmCQ6). The draft genome sequence of PmCQ2 is 2.32 Mbp and contains 2,002 protein-coding genes, 9 insertion sequence (IS) elements, and 1 prophage region. The draft genome sequence of PmCQ6 is 2.29 Mbp and contains 1,970 protein-coding genes, 2 IS elements, and 3 prophage regions. The genome alignment analysis revealed that the genome similarity between PmCQ2 and PmCQ6 is 99% with high colinearity. To identify the candidate genes responsible for virulence, the PmCQ2 and PmCQ6 were compared together with that of the published genomes of high virulent Pm36950 and PmHN06 and avirulent Pm3480 and Pm70 (capsular type F). Five genes and two insertion sequences are identified in high virulent strains but not in low virulent or avirulent strains. These results indicated that these genes or insertion sequences might be responsible for the virulence of P. multocida, providing prospective candidates for further studies on the pathogenesis and the host-pathogen interactions of P. multocida.

Download Full-text

First Report and Comparative Genomics Analysis of a blaOXA-244–Harbouring Escherichia coli Isolate Recovered in American Continent

10.20944/preprints201909.0150.v1 ◽

2019 ◽

Author(s):

Deisy J Abril ◽

Ingrid Gisell Bustos Moya ◽

Ricaurte Alejandro Marquez-Ortiz ◽

Diego Fernando Josa Montero ◽

Zayda Lorena Corredor Rozo ◽

...

Keyword(s):

Escherichia Coli ◽

Comparative Genomics ◽

Genomic Island ◽

Genomic Analysis ◽

American Continent ◽

Incompatibility Group ◽

Coli Isolate ◽

First Report ◽

E Coli ◽

Comparative Genomics Analysis

The carbapenemase OXA-244 is a derivate of OXA-48, and its detection is very difficult in laboratories. Here we report the identification and genomic analysis of an Escherichia coli isolate (28Eco12) harbouring the blaOXA-244 gene identified in Colombia, South America. The 28Eco12 isolate was identified during a retrospective study and it was recovered from a patient treated in Colombia. The complete nucleotide sequence was established using the PacBio platform. A comparative genomics analysis with other blaOXA-244–harbouring Escherichia coli strains was performed. The 28Eco12 isolate belonged to sequence type (ST) 38 and its genome was composed of two molecules, a chromosome of 5,343,367 bp and a plasmid of 92,027 bp, which belonged to the incompatibility group IncY and did not harbour resistance genes. The blaOXA-244 gene was chromosomally-encoded and mobilized by an ISR1-related Tn6237 composite transposon. Notably, this transposon was inserted and located within a new genomic island. For our knowledge this is the first report of a blaOXA-244–harbouring Escherichia coli isolate in American continent.Our results suggest that the introduction of the OXA-244-producing E. coli isolate was through clonal expansion of the ST38 pandemic clone. Other isolates producing OXA-244 could be circulating silently on the American continent.

Download Full-text