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Auteur Bailleul, D.; Stoeckel, S.; Arnaud-Haond, S.
Titre RClone: a package to identify MultiLocus Clonal Lineages and handle clonal data sets in r Type Article scientifique
Année 2016 Publication Revue Abrégée Methods Ecol. Evol.
Volume 7 Numéro 8 Pages 966-970
Mots-Clés clonal diversity; clonality; clonal population; diversity; genotype; markers; multilocus genotypes; multilocus lineages; organisms; population-genetics; program; software; spatial autocorrelation
Résumé Partially, clonal species are common in the Tree of Life. And yet, population genetic models still mostly focus on the extremes: strictly sexual versus purely asexual reproduction. Here, we present an R package built upon genclone software including new functions and several improvements. The RClone package includes functions to handle clonal data sets, allowing (i) checking for data set reliability to discriminate multilocus genotypes (MLGs), (ii) ascertainment of MLG and semi-automatic determination of clonal lineages (MLL), (iii) genotypic richness and evenness indices calculation based on MLGs or MLLs and (iv) describing several spatial components of clonality. RClone allows the one-shot analysis of multipopulation data sets without size limitation, suitable for data sets now increasingly produced through next-generation sequencing. A major improvement compared to existing software is the ability to determine the threshold to cluster similar MLGs into MLLs, based on implemented simulations of sexual events. Several functions allow data importation, conversion and exportation with adegenet, Genetix or Arlequin. RClone is provided with two vignettes to handle analysis on one (RClonequickmanual) or several populations (RCloneqmsevpops).
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Volume de collection Numéro de collection Edition
ISSN 2041-210x ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1637
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Auteur Ben-Gharbia, H.; Yahia, O.K.-D.; Amzil, Z.; Chomerat, N.; Abadie, E.; Masseret, E.; Sibat, M.; Triki, H.Z.; Nouri, H.; Laabir, M.
Titre Toxicity and Growth Assessments of Three Thermophilic Benthic Dinoflagellates (Ostreopsis cf. ovata, Prorocentrum lima and Coolia monotis) Developing in the Southern Mediterranean Basin Type Article scientifique
Année 2016 Publication Revue Abrégée Toxins
Volume 8 Numéro 10 Pages 297
Mots-Clés coastal waters; Coolia monotis; environmental-factors; growth; gulf-of-california; harmful algal blooms; marine dinoflagellate; multiple sequence alignment; new-zealand; okadaic acid; Ostreopsis cf. ovata; Prorocentrum lima; Southern Mediterranean Sea; sp-nov dinophyceae; toxicity; toxin profile
Résumé Harmful benthic dinoflagellates, usually developing in tropical areas, are expanding to temperate ecosystems facing water warming. Reports on harmful benthic species are particularly scarce in the Southern Mediterranean Sea. For the first time, three thermophilic benthic dinoflagellates (Ostreopsis cf. ovata, Prorocentrum lima and Coolia monotis) were isolated from Bizerte Bay (Tunisia, Mediterranean) and monoclonal cultures established. The ribotyping confirmed the morphological identification of the three species. Maximum growth rates were 0.59 +/- 0.08 d(-1) for O. cf. ovata, 0.35 +/- 0.01 d(-1) for C. monotis and 0.33 +/- 0.04 d(-1) for P. lima. Toxin analyses revealed the presence of ovatoxin-a and ovatoxin-b in O. cf. ovata cells. Okadaic acid and dinophysistoxin-1 were detected in P. lima cultures. For C. monotis, a chromatographic peak at 5.6 min with a mass m/z = 1061.768 was observed, but did not correspond to a mono-sulfated analogue of the yessotoxin. A comparison of the toxicity and growth characteristics of these dinoflagellates, distributed worldwide, is proposed.
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ISSN 2072-6651 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1690
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Auteur Besson, M.; Allal, F.; Chatain, B.; Vergnet, A.; Clota, F.; Vandeputte, M.
Titre Combining Individual Phenotypes of Feed Intake With Genomic Data to Improve Feed Efficiency in Sea Bass Type Article scientifique
Année 2019 Publication Revue Abrégée Front. Genet.
Volume 10 Numéro Pages
Mots-Clés Aquaculture; Feed conversation ratio; Fine phenotyping; genomic selection; Individual feed intake; Restricted feeding; selective breeding
Résumé Measuring individual feed intake of fish in farms is complex and precludes direct selective breeding for feed conversion ratio (FCR). Here, we estimated the individual FCR of 588 sea bass using individual rearing under restricted feeding. These fish were also phenotyped for their weight loss at fasting and muscle fat content as possible indirect indicators of FCR. The 588 fish were from a full factorial mating between parental lines divergently selected for high (F+) or low (F-) weight loss at fasting. The pedigree was known back to the great grandparents. A subset of 400 offspring and their ancestors were genotyped for 1,110 SNPs, which allowed estimating the genomic heritability of traits. Individual FCR and growth rate in aquarium were both heritable (genomic h² = 0.47 and 0.76, respectively) and strongly genetically correlated (-0.98), meaning that under restricted feeding, faster growing fish were more efficient. FCR in aquariums was significantly better for fish with two F- parents (1.38), worse for fish with two F+ parents (1.51) and intermediate (1.46) for crossbred fish (F+/F- or F-/F+). Muscle fat content was positively genetically correlated to growth rate in aquarium and during fasting. Thus, higher growth rate in aquariums, lower weight loss at fasting and fat content are all traits that could improve FCR in aquarium. Improving these traits would also improve FCR of fish in normal group rearing conditions, as we showed that groups composed of fish with good individual FCR were significantly more efficient in groups. The FCR of groups was also better when the fish composing the groups had, on average, lower estimated breeding values for growth rate during fasting (losing less weight). Thus, FCR in aquarium and weight loss at fasting are both promising to improve FCR of fish in groups. Finally, we showed that the reliability of estimated breeding values was higher (from +10% to +125%) with single-step genomic BLUP than with pedigree-based BLUP, showing that genomic data would enhance the accuracy of EBV prediction o in selection candidates from a limited number of sibs individually phenotyped for FCR in aquariums.
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Volume de collection Numéro de collection Edition
ISSN 1664-8021 ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 2542
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Auteur Brosset, P.; Lloret, J.; Munoz, M.; Fauvel, C.; Van Beveren, E.; Marques, V.; Fromentin, J.-M.; Menard, F.; Saraux, C.
Titre Body reserves mediate trade-offs between life-history traits: new insights from small pelagic fish reproduction Type Article scientifique
Année 2016 Publication Revue Abrégée R. Soc. Open Sci.
Volume 3 Numéro 10 Pages 160202
Mots-Clés anchovy; clutch size; daily egg-production; empirical-evidence; energy allocation; environmental variability; herring clupea-harengus; maternal effect; mediterranean sardine; northwest Mediterranean; phenotypic plasticity; sardina-pilchardus; sardine; upwelling systems
Résumé Limited resources in the environment prevent individuals from simultaneouslymaximizing all life-history traits, resulting in trade-offs. In particular, the cost of reproduction is well known to negatively affect energy investment in growth and maintenance. Here, we investigated these trade-offs during contrasting periods of high versus low fish size and body condition (before/after 2008) in the Gulf of Lions. Female reproductive allocation and performance in anchovy (Engraulis encrasicolus) and sardine (Sardina pilchardus) were examined based onmorphometric historical data from the 1970s and from 2003 to 2015. Additionally, potential maternal effects on egg quantity and quality were examined in 2014/2015. After 2008, the gonadosomatic index increased for sardine and remained steady for anchovy, while a strong decline in mean length at first maturity indicated earlier maturation for both species. Regarding maternal effects, for both species egg quantity was positively linked to fish size but not to fish lipid reserves, while the egg quality was positively related to lipid reserves. Atresia prevalence and intensity were rather low regardless of fish condition and size. Finally, estimations of total annual numbers of eggs spawned indicated a sharp decrease for sardine since 2008 but a slight increase for anchovy during the last 5 years. This study revealed a biased allocation towards reproduction in small pelagic fish when confronted with a really low body condition. This highlights that fish can maintain high reproductive investment potentially at the cost of other traits which might explain the present disappearance of old and large individuals in the Gulf of Lions.
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Volume de collection Numéro de collection Edition
ISSN 2054-5703 ISBN Médium
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Numéro d'Appel MARBEC @ alain.herve @ collection 1692
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Auteur Bui, V.N.; Nguyen, T.T.H.; Bettarel, Y.; Nguyen, T.H.T.; Pham, T.L.; Hoang, T.Y.; Nguyen, V.T.T.; Nghiem, N.M.; Wölfl, S.
Titre Genotoxicity of Chemical Compounds Identification and Assessment by Yeast Cells Transformed With GFP Reporter Constructs Regulated by the PLM2 or DIN7 Promoter Type Article scientifique
Année 2015 Publication Revue Abrégée International Journal of Toxicology
Volume 34 Numéro 1 Pages 31-43
Mots-Clés biosensor; DNA damage-inducible promoters; DNA-damaging agents; genotoxicity; gfp
Résumé Yeast cells transformed with high-copy number plasmids comprising a green fluorescent protein (GFP)-encoding gene optimized for yeast under the control of the new DIN7 or PLM2 and the established RNR2 and RAD54 promoters were used to assess the genotoxic potential of chemical compounds. The activity of potential DNA-damaging agents was investigated by genotoxicity assays and by OxoPlate assay in the presence of various test compounds. The fluorescence signal generated by GFP in response to DNA damage was related to the different concentrations of analytes and the analyte-dependent GFP synthesis. The use of distinct DNA damage-inducible promoters presents alternative genotoxicity testing strategies by selective induction of promoters in response to DNA damage. The new DIN7 and PLM2 systems show higher sensitivity than the RNR2 and RAD54 systems in detecting 4-nitroquinoline-N-oxide and actinomycin D. Both DIN7 and PLM2 systems are able to detect camptothecin while RNR2 and RAD54 systems are not. Automated laboratory systems with assay performance on 384-well microplates provide for cost-effective high-throughput screening of DNA-damaging agents, reducing compound consumption to about 53% as compared with existing eukaryotic genotoxicity bioassays.
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ISSN 1091-5818, 1092-874x ISBN Médium
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Numéro d'Appel MARBEC @ isabelle.vidal-ayouba @ collection 1419
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