Virginie Dupuy

• French Agricultural Research Centre for International Development

Multi-Locus Sequence Analysis (MLSA) of Mycoplasma capricolum subsp. capripneumoniae (Mccp) strains from Asia revealed unforeseen diversity and a central position for genotyping groups representing strains from Central/East Asia, suggesting a possible origin of contagious caprine pleuropneumonia in this continent. A better assessment of the emergen...

Contagious caprine pleuropneumonia (CCPP), caused by Mycoplasma capricolum subsp. capripneumoniae (Mccp), is a devastating disease of domestic goats and of some wild ungulate species. The disease is currently spreading in Africa and Asia and poses a serious threat to disease-free areas. A comprehensive view of the evolutionary history and dynamics...

The multiplex SNaPshot and the capillary electrophoresis-single-strand conformation polymorphism (CE-SSCP) procedures are here used for rapid and high-throughput description of the molecular variability of viral populations. Both approaches are based on (1) standard amplification of genomic sequence(s), (2) labeled primers or labeled single-strande...

Mycoplasma capricolum subsp. capripneumoniae is the etiological agent of contagious caprine pleuropneumonia. We report here the complete and annotated genome sequence of M. capricolum subsp. capripneumoniae strain 9231-Abomsa.

Motivation Among challenges that hamper reaping the benefits of genome assembly are both unfinished assemblies and the ensuing experimental costs. First, numerous software solutions for genome de novo assembly are available, each having its advantages and drawbacks, without clear guidelines as to how to choose among them. Second, these solutions pr...

We report here the draft genome sequences of Mycoplasma auris and Mycoplasma yeatsii, two species commonly isolated from the external ear canal of Caprinae.

Mycoplasma putrefaciens is one of the etiologic agents of contagious agalactia in goats. We report herein the complete genome sequence of Mycoplasma putrefaciens strain 9231.

We report here the draft genome sequences of Mycoplasma alkalescens, Mycoplasma arginini, and Mycoplasma bovigenitalium. These three species are regularly isolated from bovine clinical specimens, although their role in disease is unclear.

Mycoplasma mycoides subsp. mycoides "Small Colony" (MmmSC) is responsible for contagious bovine pleuropneumonia (CBPP) in bovidae, a notifiable disease to the World Organization for Animal Health (OIE). Although its origin is not documented, the disease was known in Europe in 1773. It reached nearly world-wide distribution in the 19(th) century thr...

Input file for BEAST analysis. Xml file generated by the BEAUTi software. This file contains all sequence data as well as informations needed by the BEAST software to perform a Bayesian evolutionary analysis such as site model, clock models, priors, operators and MCMC chain length. (XML)

Haplotype network of Mycoplasma mycoides subsp. mycoides “Small Colony” (MmmSC) sequences obtained using statistical parsimony. The cladogram was obtained with TCS from the alignment of the 139 nucleotides corresponding to the MmmSC polymorphic sites of 62 concatenated core genes. Strains KH3J and PG1T were not connected to this network because the...

Alignment of 62 concatenated core genes of 20 MmmSC strains and an Mmc outgroup. Input file for phylogenetic analysis using PhyML. (PHY)

List of Mycoplasma mycoides subsp. mycoides “Small Colony” strains studied. (TIF)

Phylogenetic tree of Mycoplasma mycoides subsp. mycoides “Small Colony” (MmmSC) sequences using parsimony analysis. The most parsimonious tree was obtained using Dnapars (Phylip package) from the alignment of the 139 nucleotides corresponding to the MmmSC polymorphic sites of 62 concatenated core genes. Strain names are colored according to the sam...

Alignment of polymorphic sites of 62 concatenated core genes from 20 MmmSC strains. Multifasta file containing only polymorphic bases, used for analysis with the PHYLIP package. (FAS)

List of MmmSC concatenated genes. (TIF)

Models of indirect (genetic) benefits sexual selection predict linkage disequilibria between genes that influence male traits and female preferences, owing to non-random mate choice or physical linkage. Such linkage disequilibria can accelerate the evolution of traits and preferences to exaggerated levels. Both theory and recent empirical findings...

This file illustrates the mapping of QTLs for developmental, male signal, and female receiver traits among linkage groups in broods Xt7 and Xt19. Each section of the file shows maps of a pair of associated linkage groups where association was possible due to common markers, or only one linkage group where common markers did not occur. Two sections...

Mycoplasma agalactiae and Mycoplasma bovis are important pathogens producing similar pathologies in small ruminants and cattle, respectively. They share many phenotypic and genotypic traits and comparison of their 16S rDNA sequences lacks sufficient resolution for phylogenetic analysis. The aim of this study was to develop a multilocus sequence typ...

A pneumonia outbreak reduced the numbers of a wild population of endangered markhors (Capra falconeri) in Tajikistan in 2010. The infection was diagnosed by histologic examination and bacteriologic testing. Mycoplasma capricolum subsp. capricolum was the sole infectious agent detected. Cross-species transmission from domestic goats may have occurre...

Table S1. GenBank accession numbers of locus sequences obtained in this study. Displayed are GenBank accession numbers corresponding to the sequences of 14 strains representing the 14 ST discriminated based on the seven new MLSA loci.

Mycoplasma capricolum subsp. capripneumoniae (Mccp) is the causative agent of contagious caprine pleuropneumonia (CCPP), a devastating disease of domestic goats. The exact distribution of CCPP is not known but it is present in Africa and the Middle East and represents a significant threat to many disease-free areas including Europe. Furthermore, CC...

Thirty-five unique partial sugarcane bacilliform virus (SCBV) sequences extending over 529 bp were identified in sugarcane samples from Guadeloupe diagnosed by Immunocapture-PCR (IC-PCR) using specific badnavirus primers. Phylogenetic analysis of these sequences along with the two known genome sequences of Sugarcane bacilliform Mor virus (SCBMV) an...

"Organization of lipoprotein gene clusters in the Mmc 95010 genome". This figure is a schematic representation of 6 lipoprotein families (A to F) found in the genome of strain 95010.

"Peculiar Mmc genomic locus encoding predicted surface proteins". This figure is a schematic representation of the locus and homologies with M. agalactiae or M. capricolum subsp. capricolum genes.

"organization of a Mmc-specific lipoprotein gene clusters in the Mmc 95010 genome". This figure is a schematic representation of a lipoprotein family found in strain 95010 genome but not in the published MmmSC genomes.

"PCR primers used during this study". This additional table lists the names and sequences of primers used in the study.

"Comparison of plasmids from the mycoides cluster". This figure depicts the results of a three-way BLASTN comparison of three mycoplasma plasmid sequences using the Artemis Comparison Tool [71]

"List of CDS in Mmc strains GM12 and 95010 showing less than 90% similarity with each other". This additional table lists the names of genes that are not highly similar in two strains belonging to the same subspecies, M. mycoides subsp. capri.

"Comparison of related plasmid and ICE sequences in Mmc 95010". This figure describes the positions and sequences shared by the integrative conjugative elements copies and the plasmid that was characterized in the same strain.

"List of gene clusters identified as orthologous". This additional table lists the names of genes found orthologous by the Microbial Genome Database for Comparative Analysis http://mbgd.genome.ad.jp/

The Mycoplasma mycoides cluster consists of five species or subspecies that are ruminant pathogens. One subspecies, Mycoplasma mycoides subspecies mycoides Small Colony (MmmSC), is the causative agent of contagious bovine pleuropneumonia. Its very close relative, Mycoplasma mycoides subsp. capri (Mmc), is a more ubiquitous pathogen in small ruminan...

We characterized 10 variable microsatellite loci in the freshwater snail Biomphalaria kuhniana, as well as conditions for multiplexing and co-loading sets of loci. Two to five alleles were detected per locus over the two studied populations in Venezuela. High inbreeding coefficients suggest high selfing rates. Cross-species amplification provided s...

We characterized eight microsatellite loci to study spatial and temporal population structure of Pelodytes punctatus, a European anuran that has a peculiar breeding pattern among amphibians. The eight loci proved to be highly polymorphic with the number of alleles per locus ranging from two to 15 within two populations. Cross-amplification indicate...

Heritabilities and genetic correlations of fertility (FERT) as well as of susceptibilities to early (EEM), medium (MEM), and late (LEM) embryonic mortalities conditional on fertility and survival to earlier stage(s) of embryonic mortality were estimated with a general linear model using a logistic link function on 59,794 eggs obtained from 6,480 he...