Éditeur(s) : HAL CCSD Society for Molecular Biology and Evolution
Résumé : International audience
Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the USA. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of twenty V. cholerae and four V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as four clinical V. metoecus strains were sequenced and compared to reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. V. metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin co-regulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. V. metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.
ISSN: 1759-6653

Droits : http://creativecommons.org/licenses/by/
hal-01264332
http://hal.upmc.fr/hal-01264332
http://hal.upmc.fr/hal-01264332/document
http://hal.upmc.fr/hal-01264332/file/Genome%20Biol%20Evol-2015-Orata-gbe_evv193.pdf
DOI : 10.1093/gbe/evv193

Éditeur(s) : HAL CCSD Medknow Publications
Résumé : International audience
Multiple regions of the genome have been associated with the risk of prostate cancer in Caucasians, particularly including several polymorphisms located at 8q24. Region 2 of 8q24 has been repeatedly found to be associated with the risk of prostate cancer among men of African descent, although one study performed in the Caribbean island of Jamaica did not report this finding. In this study, the single nucleotide polymorphism rs16901979, located in region 2 of 8q24, was genotyped in 498 cases of histologically confirmed prostate cancer and 541 controls from the French Caribbean islands of Guadeloupe, where the population is largely of African descent. The AA genotype and the A allele at rs16901979 were associated with elevated risks of prostate cancer (odds ratios [ORs] = 1.84, 95% confidence interval [95% CI] = 1.26-2.69, P = 0.002 and OR = 1.36, 95% CI = 1.13-1.64, P = 0.001, respectively). Following stratification of the patients by disease aggressiveness, as defined by the Gleason score, the pooled genotypes AC + AA were associated with a higher risk of a Gleason score ≥7 at diagnosis (OR = 1.79, 95% CI = 1.17-2.73, P = 0.007). In summary, the A allele at rs16901979 was associated with the risk of prostate cancer in the Caribbean population of Guadeloupe, confirming its involvement in populations of African descent. Moreover, our study provides the first evidence of an association between this variant and the risk of aggressive prostate cancer.
ISSN: 1008-682X

Droits : http://creativecommons.org/licenses/by-nc-sa/
hal-01118552
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552/document
https://hal-univ-rennes1.archives-ouvertes.fr/hal-01118552/file/AsianJAndrol171117-1705456_044414.pdf
DOI : 10.4103/1008-682X.135127

Éditeur(s) : HAL CCSD Springer
Résumé : International audience
Total genomic DNA of eight colonies for each of the two species, Acropora muricata and Porites lutea, sampled on the west coast of Reunion Island, was isolated using DNeasy Blood & Tissue kit (Qiagen™) following the manufacturer’s instructions and sent to GenoScreen, Lille, France (www.genoscreen.fr).
ISSN: 1877-7252

hal-01254248
https://hal.archives-ouvertes.fr/hal-01254248
https://hal.archives-ouvertes.fr/hal-01254248/document
https://hal.archives-ouvertes.fr/hal-01254248/file/G%C3%A9lin%20et%20al.%20-%202015%20-%20Isolation%20and%20characterization%20of%2022%20microsatellit_hal.pdf
DOI : 10.1007/s12686-015-0493-8

Éditeur(s) : HAL CCSD Frontiers Media
Résumé : The disease, Heartwater, caused by the Anaplasmataceae E. ruminantium, represents a major problem for tropical livestock and wild ruminants. Up to now, no effective vaccine has been available due to a limited cross protection of vaccinal strains on field strains and a high genetic diversity of Ehrlichia ruminantium within geographical locations. To address this issue, we inferred the genetic diversity and population structure of 194 E. ruminantium isolates circulating worldwide using Multilocus Sequence Typing based on lipA, lipB, secY, sodB, and sucA genes. Phylogenetic trees and networks were generated using BEAST and SplitsTree, respectively, and recombination between the different genetic groups was tested using the PHI test for recombination. Our study reveals the repeated occurrence of recombination between E. ruminantium strains, suggesting that it may occur frequently in the genome and has likely played an important role in the maintenance of genetic diversity and the evolution of E. ruminantium. Despite the unclear phylogeny and phylogeography, E. ruminantium isolates are clustered into two main groups: Group 1 (West Africa) and a Group 2 (worldwide) which is represented by West, East, and Southern Africa, Indian Ocean, and Caribbean strains. Some sequence types are common between West Africa and Caribbean and between Southern Africa and Indian Ocean strains. These common sequence types highlight two main introduction events due to the movement of cattle: from West Africa to Caribbean and from Southern Africa to the Indian Ocean islands. Due to the long branch lengths between Group 1 and Group 2, and the propensity for recombination between these groups, it seems that the West African clusters of Subgroup 2 arrived there more recently than the original divergence of the two groups, possibly with the original waves of domesticated ruminants that spread across the African continent several thousand years ago.
ISSN: 2235-2988

hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501
https://hal.archives-ouvertes.fr/hal-01594501/document
https://hal.archives-ouvertes.fr/hal-01594501/file/paper_MLST_ER_2016_%7B51027B58-C2C7-41C8-9746-BD8A9F387C87%7D.pdf
DOI : 10.3389/fcimb.2016.00111

Éditeur(s) : HAL CCSD Public Library of Science
Résumé : International audience
We studied the diversity within the former genus Gymnangium in the South West IndianOcean by using an integrative approach of both traditional (morphology-based) and modernmolecular taxonomy. Nine species were recorded in the material collected. A total of 97 16Smitochondrial DNA sequences and 54 Calmodulin nuclear sequences from eight Gymnangium/Taxella species were analyzed. We found both morphological and molecular differencesin the studied Gymnangium species that make it necessary to split the genus. It isproposed to revalidate the genus Taxella which is currently regarded as a synonym ofGymnangium. Two species of the genus Taxella (T. eximia and T. gracilicaulis), until nowregarded as distinct species based on morphological characteristics, cluster together in onephylogenetic clade. Possible explanations are discussed. Two species from Madagascarnew to science are herein described and rare species from the Indian Ocean islands are redescribed.
ISSN: 1932-6203

hal-01564043
https://hal-univ-perp.archives-ouvertes.fr/hal-01564043
DOI : 10.1371/journal.pone.0174244