scholarly journals Multiple Genome Comparison within a Bacterial Species Reveals a Unit of Evolution Spanning Two Adjacent Genes in a Tandem Paralog Cluster

2008 ◽  
Vol 25 (11) ◽  
pp. 2457-2473 ◽  
Author(s):  
T. Tsuru ◽  
I. Kobayashi
Keyword(s):  
Bacterial Species ◽  
Genome Comparison ◽  
Multiple Genome

Sybil: Methods and Software for Multiple Genome Comparison and Visualization

2007 ◽  
pp. 93-108 ◽  
Author(s):  
Jonathan Crabtree ◽  
Samuel V. Angiuoli ◽  
Jennifer R. Wortman ◽  
Owen R. White
Keyword(s):  
Genome Comparison ◽  
Multiple Genome

scholarly journals TWO PLUS TWO DOES NOT EQUAL THREE: STATISTICAL TESTS FOR MULTIPLE GENOME COMPARISON

2008 ◽  
Vol 06 (01) ◽  
pp. 1-22 ◽  
Author(s):  
NARAYANAN RAGHUPATHY ◽  
ROSE HOBERMAN ◽  
DANNIE DURAND
Keyword(s):  
Comparative Genomics ◽  
Large Scale ◽  
Statistical Tests ◽  
Gene Clusters ◽  
Genome Comparison ◽  
Pairwise Comparisons ◽  
Multiple Genome ◽  
Number Of Genes ◽  
Multiple Species ◽  
Combine Evidence

Gene clusters that span three or more chromosomal regions are of increasing importance, yet statistical tests to validate such clusters are in their infancy. Current approaches either conduct several pairwise comparisons or consider only the number of genes that occur in all of the regions. In this paper, we provide statistical tests for clusters spanning exactly three regions based on genome models of typical comparative genomics problems, including analysis of conserved linkage within multiple species and identification of large-scale duplications. Our tests are the first to combine evidence from genes shared among all three regions and genes shared between pairs of regions. We show that our tests of clusters spanning three regions are more sensitive than existing approaches, and can thus be used to identify more diverged homologous regions.

scholarly journals A Whole Genome Pairwise Comparative and Functional Analysis of Geobacter sulfurreducens PCA

2013 ◽  
Vol 2013 ◽  
pp. 1-6 ◽  
Author(s):  
Ashok Selvaraj ◽  
Subazini Thankaswamy Kosalai ◽  
Rajadurai Chinnasamy Perumal ◽  
Subhashini Pitchai ◽  
Gopal Ramesh Kumar
Keyword(s):  
Abc Transporters ◽  
Bacterial Species ◽  
Geobacter Sulfurreducens ◽  
Electricity Production ◽  
Genome Comparison ◽  
Whole Genome ◽  
Functional Prediction ◽  
Conserved Genes ◽  
Flagellar Proteins ◽  
Genome Analyses

Geobacter species are involved in electricity production, bioremediations, and various environmental friendly activities. Whole genome comparative analyses of Geobacter sulfurreducens PCA, Geobacter bemidjiensis Bem, Geobacter sp. FRC-32, Geobacter lovleyi SZ, Geobacter sp. M21, Geobacter metallireducens GS-15, Geobacter uraniireducens Rf4 have been made to find out similarities and dissimilarities among them. For whole genome comparison of Geobacter species, an in-house tool, Geobacter Comparative Genomics Tool (GCGT) has been developed using BLASTALL program, and these whole genome analyses yielded conserved genes and they are used for functional prediction. The conserved genes identified are about 2184 genes, and these genes are classified into 14 groups based on the pathway information. Functions for 74 hypothetical proteins have been predicted based on the conserved genes. The predicted functions include pilus type proteins, flagellar proteins, ABC transporters, and other proteins which are involved in electron transfer. A phylogenetic tree from 16S rRNA of seven Geobacter species showed that G. sulfurreducens PCA is closely related to G. metallireducens GS-15 and G. lovleyi SZ. For evolutionary study, acetate kinase protein is used, which showed closeness to Pelobacter propionicus, Pelobacter carbinolicus, and Deferribacteraceae family bacterial species. These results will be useful to enhance electricity production by using biotechnological approaches.

scholarly journals An alternative approach to multiple genome comparison

2011 ◽  
Vol 39 (15) ◽  
pp. e101-e101 ◽  
Author(s):  
Alban Mancheron ◽  
Raluca Uricaru ◽  
Eric Rivals
Keyword(s):  
Genome Comparison ◽  
Multiple Genome ◽  
Alternative Approach

scholarly journals Chaining algorithms for multiple genome comparison

2005 ◽  
Vol 3 (2-4) ◽  
pp. 321-341 ◽  
Author(s):  
Mohamed Ibrahim Abouelhoda ◽  
Enno Ohlebusch
Keyword(s):  
Genome Comparison ◽  
Multiple Genome

scholarly journals Culturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates

2020 ◽  
Vol 8 (10) ◽  
pp. 1522
Author(s):  
Pamela Afouda ◽  
Grégory Dubourg ◽  
Anthony Levasseur ◽  
Pierre-Edouard Fournier ◽  
Jeremy Delerce ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Antimicrobial Agents ◽  
Bacterial Species ◽  
Acquired Resistance ◽  
Antibiotic Resistance Genes ◽  
Resistance Mechanisms ◽  
Genome Comparison ◽  
Antibiotics Use ◽  
High Level

Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.

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