Publications by authors named "J Le Luyer"

18 Publications

Dual RNAseq highlights the kinetics of skin microbiome and fish host responsiveness to bacterial infection.

Anim Microbiome 2021 May 7;3(1):35. Epub 2021 May 7.

Ifremer, IRD, Institut Louis-Malardé, Univ Polynésie Française, EIO, F-98719 Taravao, Tahiti, Polynésie Française.

Background: Tenacibaculum maritimum is a fish pathogen known for causing serious damage to a broad range of wild and farmed marine fish populations worldwide. The recently sequenced genome of T. maritimum strain NCIMB 2154 provided unprecedented information on the possible molecular mechanisms involved in the virulence of this species. However, little is known about the dynamic of infection in vivo, and information is lacking on both the intrinsic host response (gene expression) and its associated microbiota. Here, we applied complementary omic approaches, including dual RNAseq and 16S rRNA gene metabarcoding sequencing using Nanopore and short-read Illumina technologies to unravel the host-pathogen interplay in an experimental infection system using the tropical fish Platax orbicularis as model.

Results: We showed that the infection of the host is characterised by an enhancement of functions associated with antibiotic and glucans catabolism functions but a reduction of sulfate assimilation process in T. maritimum. The fish host concurrently displays a large panel of immune effectors, notably involving innate response and triggering acute inflammatory response. In addition, our results suggest that fish activate an adaptive immune response visible through the stimulation of T-helper cells, Th17, with congruent reduction of Th2 and T-regulatory cells. Fish were, however, largely sensitive to infection, and less than 25% survived after 96 hpi. These surviving fish showed no evidence of stress (cortisol levels) or significant difference in microbiome diversity compared with controls at the same sampling time. The presence of T. maritimum in resistant fish skin and the total absence of any skin lesions suggest that these fish did not escape contact with the pathogen, but rather that some mechanisms prevented pathogens entry. In resistant individuals, we detected up-regulation of specific immune-related genes differentiating resistant individuals from controls at 96 hpi, which suggests a possible genomic basis of resistance, although no genetic variation in coding regions was found.

Conclusion: Here we focus in detail on the interplay between common fish pathogens and host immune response during experimental infection. We further highlight key actors of defence response, pathogenicity and possible genomic bases of fish resistance to T. maritimum.
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http://dx.doi.org/10.1186/s42523-021-00097-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8106148PMC
May 2021

Assessing the effects of genotype-by-environment interaction on epigenetic, transcriptomic, and phenotypic response in a Pacific salmon.

G3 (Bethesda) 2021 Feb;11(2)

Fisheries and Oceans Canada, West Vancouver, BC V7V 1N6, Canada.

Genotype-by-environment (GxE) interactions are non-parallel reaction norms among individuals with different genotypes in response to different environmental conditions. GxE interactions are an extension of phenotypic plasticity and consequently studying such interactions improves our ability to predict effects of different environments on phenotype as well as the fitness of genetically distinct organisms and their capacity to interact with ecosystems. Growth hormone transgenic coho salmon grow much faster than non-transgenics when raised in tank environments, but show little difference in growth when reared in nature-like streams. We used this model system to evaluate potential mechanisms underlying this growth rate GxE interaction, performing RNA-seq to measure gene transcription and whole-genome bisulfite sequencing to measure gene methylation in liver tissue. Gene ontology (GO) term analysis revealed stress as an important biological process potentially influencing growth rate GxE interactions. While few genes with transcription differences also had methylation differences, in promoter or gene regions, many genes were differentially methylated between tank and stream environments. A GO term analysis of differentially methylated genes between tank and stream environments revealed increased methylation in the stream environment of more than 95% of the differentially methylated genes, many with biological processes unrelated to liver function. The lower nutritional condition of the stream environment may cause increased negative regulation of genes less vital for liver tissue function than when fish are reared in tanks with unlimited food availability. These data show a large effect of rearing environment both on gene expression and methylation, but it is less clear that the detected epigenetic marks are responsible for the observed altered growth and physiological responses.
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http://dx.doi.org/10.1093/g3journal/jkab021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8022943PMC
February 2021

Tracing key genes associated with the Pinctada margaritifera albino phenotype from juvenile to cultured pearl harvest stages using multiple whole transcriptome sequencing.

BMC Genomics 2020 Sep 25;21(1):662. Epub 2020 Sep 25.

Ifremer, UMR EIO 241, Centre du Pacifique, BP 49, 98719, Taravao, Tahiti, Polynéise française, France.

Background: Albino mutations are commonly observed in the animal kingdom, including in bivalves. In the black-lipped pearl oyster Pinctada margaritifera, albino specimens are characterized by total or partial absence of colouration resulting in typical white shell phenotype expression. The relationship of shell colour with resulting cultured pearl colour is of great economic interest in P. margaritifera, on which a pearl industry is based. Hence, the albino phenotype provides a useful way to examine the molecular mechanisms underlying pigmentation.

Results: Whole transcriptome RNA-sequencing analysis comparing albino and black wild-type phenotypes at three stages over the culture cycle of P. margaritifera revealed a total of 1606, 798 and 187 differentially expressed genes in whole juvenile, adult mantle and pearl sac tissue, respectively. These genes were found to be involved in five main molecular pathways, tightly linked to known pigmentation pathways: melanogenesis, calcium signalling pathway, Notch signalling pathway, pigment transport and biomineralization. Additionally, significant phenotype-associated SNPs were selected (N = 159), including two located in the Pif biomineralization gene, which codes for nacre formation. Interestingly, significantly different transcript splicing was detected between juvenile (N = 1366) and adult mantle tissue (N = 313) in, e.g., the tyrosinase Tyr-1 gene, which showed more complex regulation in mantle, and the Notch1 encoding gene, which was upregulated in albino juveniles.

Conclusion: This multiple RNA-seq approach provided new knowledge about genes associated with the P. margaritifera albino phenotype, highlighting: 1) new molecular pathways, such as the Notch signalling pathway in pigmentation, 2) associated SNP markers with biomineraliszation gene of interest like Pif for marker-assisted selection and prevention of inbreeding, and 3) alternative gene splicing for melanin biosynthesis implicating tyrosinase.
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http://dx.doi.org/10.1186/s12864-020-07015-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7517651PMC
September 2020

Microplastics induce dose-specific transcriptomic disruptions in energy metabolism and immunity of the pearl oyster Pinctada margaritifera.

Environ Pollut 2020 Nov 8;266(Pt 3):115180. Epub 2020 Jul 8.

Ifremer, Institut Louis-Malardé, IRD, Univ Polynésie Française, EIO, F-98719, Taravao, Tahiti, Polynésie française, France. Electronic address:

A combined approach integrating bioenergetics and major biological activities is essential to properly understand the impact of microplastics (MP) on marine organisms. Following experimental exposure of polystyrene microbeads (micro-PS of 6 and 10 μm) at 0.25, 2.5, and 25 μg L, which demonstrated a dose-dependent decrease of energy balance in the pearl oyster Pinctada margaritifera, a transcriptomic study was conducted on mantle tissue. Transcriptomic data helped us to decipher the molecular mechanisms involved in P. margaritifera responses to micro-PS and search more broadly for effects on energetically expensive maintenance functions. Genes related to the detoxification process were impacted by long-term micro-PS exposure through a decrease in antioxidant response functioning, most likely leading to oxidative stress and damage, especially at higher micro-PS doses. The immune response was also found to be dose-specific, with a stress-related activity stimulated by the lowest dose present after a 2-month exposure period. This stress response was not observed following exposure to higher doses, reflecting an energy-limited capacity of pearl oysters to cope with prolonged stress and a dramatic shift to adjust to pessimum conditions, mostly limited and hampered by a lowered energetic budget. This preliminary experiment lays the foundation for exploring pathways and gene expression in P. margaritifera, and marine mollusks in general, under MP exposure. We also propose a conceptual framework to properly assess realistic MP effects on organisms and population resilience in future investigations.
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http://dx.doi.org/10.1016/j.envpol.2020.115180DOI Listing
November 2020

Mapping of Adaptive Traits Enabled by a High-Density Linkage Map for Lake Trout.

G3 (Bethesda) 2020 06 1;10(6):1929-1947. Epub 2020 Jun 1.

Department of Integrative Biology, Michigan State University, East Lansing MI.

Understanding the genomic basis of adaptative intraspecific phenotypic variation is a central goal in conservation genetics and evolutionary biology. Lake trout () are an excellent species for addressing the genetic basis for adaptive variation because they express a striking degree of ecophenotypic variation across their range; however, necessary genomic resources are lacking. Here we utilize recently-developed analytical methods and sequencing technologies to (1) construct a high-density linkage and centromere map for lake trout, (2) identify loci underlying variation in traits that differentiate lake trout ecophenotypes and populations, (3) determine the location of the lake trout sex determination locus, and (4) identify chromosomal homologies between lake trout and other salmonids of varying divergence. The resulting linkage map contains 15,740 single nucleotide polymorphisms (SNPs) mapped to 42 linkage groups, likely representing the 42 lake trout chromosomes. Female and male linkage group lengths ranged from 43.07 to 134.64 centimorgans, and 1.97 to 92.87 centimorgans, respectively. We improved the map by determining coordinates for 41 of 42 centromeres, resulting in a map with 8 metacentric chromosomes and 34 acrocentric or telocentric chromosomes. We use the map to localize the sex determination locus and multiple quantitative trait loci (QTL) associated with intraspecific phenotypic divergence including traits related to growth and body condition, patterns of skin pigmentation, and two composite geomorphometric variables quantifying body shape. Two QTL for the presence of vermiculations and spots mapped with high certainty to an arm of linkage group Sna3, growth related traits mapped to two QTL on linkage groups Sna1 and Sna12, and putative body shape QTL were detected on six separate linkage groups. The sex determination locus was mapped to Sna4 with high confidence. Synteny analysis revealed that lake trout and congener Arctic char () are likely differentiated by three or four chromosomal fissions, possibly one chromosomal fusion, and 6 or more large inversions. Combining centromere mapping information with putative inversion coordinates revealed that the majority of detected inversions differentiating lake trout from other salmonids are pericentric and located on acrocentric and telocentric linkage groups. Our results suggest that speciation and adaptive divergence within the genus may have been associated with multiple pericentric inversions occurring primarily on acrocentric and telocentric chromosomes. The linkage map presented here will be a critical resource for advancing conservation oriented genomic research on lake trout and exploring chromosomal evolution within and between salmonid species.
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http://dx.doi.org/10.1534/g3.120.401184DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7263693PMC
June 2020