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Avarre, J. C., Dugué, R., Alonso, P., Diombokho, A., Joffrois, C., Faivre, N., et al. (2013). Analysis of the black-chinned tilapia Sarotherodon melanotheron heudelotii reproducing under a wide range of salinities: from RNA-seq to candidate genes. Molecular Ecology Resources, .
Résumé: The black-chinned tilapia Sarotherodon melanotheron heudelotii is an ecologically appealing model as it shows exceptional adaptive capacities, especially with regard to salinity. In spite of this, this species is devoid of genomic resources, which impedes the understanding of such remarkable features. De novo assembly of transcript sequences produced by next-generation sequencing technologies offers a rapid approach to obtain expressed gene sequences for non-model organisms. It also facilitates the development of quantitative real-time PCR (qPCR) assays for analysing gene expression under different environmental conditions. Nevertheless, obtaining accurate and reliable qPCR results from such data requires a number of validations prior to interpretation. The transcriptome of S. melanotheron was sequenced to discover transcripts potentially involved in the plasticity of male reproduction in response to salinity variations. A set of 54 candidate and reference genes was selected through a digital gene expression (DGE) approach, and a de novo qPCR assay using these genes was validated for further detailed expression analyses. A user-friendly web interface was created for easy handling of the sequence data. This sequence collection represents a major transcriptomic resource for S. melanotheron and will provide a useful tool for functional genomics and genetics studies.
Mots-Clés: Gene expression; Tilapia; non-model organism; reference gene; salinity; spermatogenesis
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Barberan, A., Fernandez-Guerra, A., Auguet, J. C., Galand, P. E., & Casamayor, E. O. (2011). Phylogenetic ecology of widespread uncultured clades of the Kingdom Euryarchaeota. Mol Ecol, 20(9), 1988–1996.
Résumé: Despite its widespread distribution and high levels of phylogenetic diversity, microbes are poorly understood creatures. We applied a phylogenetic ecology approach in the Kingdom Euryarchaeota (Archaea) to gain insight into the environmental distribution and evolutionary history of one of the most ubiquitous and largely unknown microbial groups. We compiled 16S rRNA gene sequences from our own sequence libraries and public genetic databases for two of the most widespread mesophilic Euryarchaeota clades, Lake Dagow Sediment (LDS) and Rice Cluster-V (RC-V). The inferred population history indicated that both groups have undergone specific nonrandom evolution within environments, with several noteworthy habitat transition events. Remarkably, the LDS and RC-V groups had enormous levels of genetic diversity when compared with other microbial groups, and proliferation of sequences within each single clade was accompanied by significant ecological differentiation. Additionally, the freshwater Euryarchaeota counterparts unexpectedly showed high phylogenetic diversity, possibly promoted by their environmental adaptability and the heterogeneous nature of freshwater ecosystems. The temporal phylogenetic diversification pattern of these freshwater Euryarchaeota was concentrated both in early times and recently, similarly to other much less diverse but deeply sampled archaeal groups, further stressing that their genetic diversity is a function of environment plasticity. For the vast majority of living beings on Earth (i.e. the uncultured microorganisms), how they differ in the genetic or physiological traits used to exploit the environmental resources is largely unknown. Inferring population history from 16S rRNA gene-based molecular phylogenies under an ecological perspective may shed light on the intriguing relationships between lineage, environment, evolution and diversity in the microbial world.
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Dalongeville, A., Benestan, L., Mouillot, D., Lobreaux, S., & Manel, S. (2018). Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus). BMC Genomics, 19, 217.
Résumé: Background: Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species. Results: Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method. Conclusion: The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment.
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Denis, M., Thyssen, M., Martin, V., Manca, B., & Vidussi, F. (2010). Ultraphytoplankton basin-scale distribution in the eastern Mediterranean Sea in winter: link to hydrodynamism and nutrients. Biogeosciences, 7(7), 2227–2244.
Résumé: The basin-scale distribution of ultraphytoplankton (< 10 mu m) was determined in the upper 200 m of the eastern Mediterranean Sea during the winter season. Four clusters were resolved by flow cytometry on the basis of their optical properties and identified as Synechococcus, Prochlorococcus, pico- (< 3 mu m) and nanoeukaryotes (3-10 mu m). Synechococcus was the most abundant population (maximum abundance of about 37 000 cells cm(-3)) and contributed up to 67.7% to the overall ultraphytoplanktonic carbon biomass, whereas the contribution of Prochlorococcus never exceeded 6.5%. The maximum integrated carbon biomass was 1763, 453, 58 and 571 mg C m(-2) for nanoeukaryotes, picoeukaryotes, Prochlorococcus and Synechococcus respectively. Water mass properties were analyzed on the basis of temperature and salinity distributions in order to account for the general circulation and locate the main hydrodynamic structures (fronts, gyres, transition between western and eastern basins). The effect of the main hydrodynamic structures and nutrients on the ultraphytoplankton distribution was investigated. No positive correlation between nutrients and phytoplankton could be established when considering large scales. However, below 50 m depth, nutrient ratios between particular stations were correlated to corresponding density ratios. In contrast, significant relationships were found between Synechococcus abundance and density, resulting from the impact of a gyre in southern Adriatic basin and a thermohaline front in the Ionian basin. A significant relationship was also found between picoeukaryotes and salinity in the comparison of western and eastern Mediterranean Sea.
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Durand, J. D., Shen, K. N., Chen, W. J., Jamandre, B. W., Blel, H., Diop, K., et al. (2012). Systematics of the grey mullets (Teleostei: Mugiliformes: Mugilidae): Molecular phylogenetic evidence challenges two centuries of morphology-based taxonomy. Mol. Phylogenet. Evol., 64(1), 73–92.
Résumé: The family Mugilidae comprises mainly coastal marine species that a:e widely distributed in all tropical, subtropical and temperate seas. Mugilid species are generally considered to be ecologically important and they are a major food resource for human populations in certain parts of the world. The taxonomy and systematics of the Mugilidae are still much debated and based primarily on morphological characters. In this study, we provide the first comprehensive molecular systematic account of the Mugilidae using phylogenetic analyses of nucleotide sequence variation at three mitochondrial loci (16S rRNA, cytochrome oxidase 1, and cytochrome b) for 257 individuals from 55 currently recognized species. The study covers all 20 mugilid genera currently recognized as being valid. The family comprises seven major lineages that radiated early on from the ancestor to all current forms. All genera that were represented by two species or more, except Cestraeus, turned out to be paraphyletic or polyphyletic. Thus, the present phylogenetic results generally disagree with the current taxonomy at the genus level and imply that the anatomical characters used for the systematics of the Mugilidae may be poorly informative phylogenetically. The present results should provide a sound basis for a taxonomic revision of the mugilid genera. A proportion of the species with large distribution ranges (including Moolgarda seheli, Mugil cephalus and M. curema) appear to consist of cryptic species, thus warranting further taxonomic and genetic work at the infra-generic level. (c) 2012 Elsevier Inc. All rights reserved.
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