SalmoBase: an integrated molecular data resource for Salmonid species

Samy, Jeevan Karloss Antony; Mulugeta, Teshome Dagne; Nome, Torfinn; Sandve, Simen Rød; Grammes, Fabian; Kent, Matthew; Lien, Sigbjørn; Våge, Dag Inge

doi:10.1186/s12864-017-3877-1

Cited by 51 publications

(47 citation statements)

References 7 publications

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“…Orthologs of the transcripts in salmon (Salmo salar) and rainbow trout (Oncorhynchus mykiss) mRNA and protein sequences were found using blastn and blastx respectively (Altschul et al 1990). Annotation from NCBI Salmo salar Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_euk/Salmo_salar/ 100/, retrieved 2015-12-17) and SalmoBase (Samy et al 2017, http://salmobase.org/, version from 2015-09-18) were both used for salmon and annotation for rainbow trout came from Berthelot et al (2014Berthelot et al ( , http://www.genoscope.cns.fr/trout/data/, version from 2014. Only the best match was retained for each reference database.…”

Section: Transcriptome Assembly Abundance Estimation and Annotationmentioning

confidence: 99%

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

Guðbrandsson

Kapralova

Franzdóttir

et al. 2018

Preprint

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The availability of diverse ecological niches can promote adaptation of trophic specializations and related traits, as has been repeatedly observed in evolutionary radiations of freshwater fish. The role of genetics, environment and history in ecologically driven divergence and adaptation, can be studied on adaptive radiations or populations showing ecological polymorphism. Salmonids, especially the Salvelinus genus, are renowned for both phenotypic diversity and polymorphism. Arctic charr (Salvelinus alpinus) invaded Icelandic streams during the glacial retreat (about 10,000 years ago) and exhibits many instances of sympatric polymorphism. Particularly well studied are the four morphs in Lake Þingvallavatn in Iceland. The small benthic (SB), large benthic (LB), planktivorous (PL) and piscivorous (PI) charr differ in many regards, including size, form and life history traits. To investigate relatedness and genomic differentiation between morphs we identified variable sites from RNA-sequencing data from three of those morphs, and verified 22 variants in population samples. The data reveal genetic differences between the morphs, with the two benthic morphs being more similar and the PL-charr more genetically different. The markers with high differentiation map to all linkage groups, suggesting ancient and pervasive genetic separation of these three morphs. Furthermore, GO analyses suggest differences in collagen metabolism, odontogenesis and sensory systems between PL-charr and the benthic morphs. Genotyping in population samples from all four morphs confirms the genetic separation and indicates that the PI-charr are less genetically distinct than the other three morphs. The genetic separation of the other three morphs indicates certain degree of reproductive isolation. The extent of gene flow between the morphs and the nature of reproductive barriers between them remain to be elucidated.

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Section: Transcriptome Assembly Abundance Estimation and Annotationmentioning

confidence: 99%

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

Guðbrandsson

Kapralova

Franzdóttir

et al. 2018

Preprint

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“…The annotations for the rainbow trout genome were obtained from (Berthelot et al, 2014), (http://www.genoscope.cns.fr/trout/data/, version from 2014-05-19). The annotation for the salmon genome came from two different sources; NCBI Salmo salar Annotation Release 100 (https://www.ncbi.nlm.nih.gov/genome/annotation_ euk/Salmo_salar/100/, retrieved 2015-12-17) and SalmoBase (Samy et al, 2017, http:// salmobase.org/, version from 2015-09-18). For each reference dataset we only retained the best 6/28 match for each transcript.…”

Section: Assembly Abundance Estimation and Annotationmentioning

confidence: 99%

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Guðbrandsson

Franzdóttir

Kristjánsson

et al. 2017

Preprint

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Phenotypic differences between closely related taxa or populations can arise through genetic variation or be environmentally induced, in both cases leading to altered transcription of genes during the structural and functional development of the body. Comparative developmental studies of closely related species or variable populations of the same species can help to elucidate the molecular mechanisms related to population divergence and speciation. Studies of Arctic charr (Salvelinus alpinus) and related salmonids have revealed considerable phenotypic variation among populations and in Arctic charr many cases of extensive variation within lakes (resource polymorphism) have been recorded. One example is the four Arctic charr morphs in the ∼10.000 year old Lake Thingvallavatn, which differ in numerous morphological and life history traits. We set out to investigate the molecular and developmental roots of this polymorphism by studying gene expression in embryos of three of the morphs reared in a common garden set-up. We performed RNA-sequencing, de-novo transcriptome assembly and compared gene expression among morphs during a timeframe in early development. Expectedly, developmental time was the predominant explanatory variable. As the data were affected by RNA-degradation, an estimate of 3'-bias was the second most common explanatory variable. Morph, both as a independent variable and as interaction with developmental time, affected the expression of numerous transcripts. The majority of transcripts with significant morph effects separated the limnetic and the benthic morphs. However, gene ontology analyses did not reveal clear functional enrichment of transcripts between groups. Verification via qPCR confirmed differential expression of several genes between the morphs, including regulatory genes such as Arid4a and Tsn. The data are consistent with a scenario where genetic divergence has contributed to differential expression of multiple genes and systems during early development of these sympatric Arctic charr morphs.

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“…We first made comparisons between treated and untreated individuals using both an a priori list of reference genes and a standard discovery‐based gene identification pipeline. We generated a list of a priori genes predicted to be differentially expressed between treated and untreated samples using four criteria: (a) genes associated with thiamine‐related biological process gene ontology (GO) terms (any line containing “thiamine” in Ssal_ICSASG_v2_GOAccession.txt downloaded from SalmoBase [Samy et al, ] on June 28, 2018), (b) genes encoding thiamine diphosphate (TDP)‐dependent enzymes, (c) genes encoding enzymes that contain a TDP binding site (NCBI conserved protein domain family “TPP_enzymes”), and (d) genes included in the Salmo salar thiamine metabolism pathway in the NCBI BioSystems Database (BSID: 1429556).…”

Section: Methodsmentioning

confidence: 99%

Among‐family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish

et al. 2019

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Variation in among‐family transcriptional responses to different environmental conditions can help to identify adaptive genetic variation, even prior to a selective event. Coupling differential gene expression with formal survival analyses allows for the disentanglement of treatment effects, required for understanding how individuals plastically respond to environmental stressors, from the adaptive genetic variation responsible for differential survival. We combined these two approaches to investigate responses to an emerging conservation issue, thiamine (vitamin B1) deficiency, in a threatened population of Atlantic salmon (Salmo salar). Thiamine is an essential vitamin that is increasingly limited in many ecosystems. In Lake Champlain, Atlantic salmon cannot acquire thiamine in sufficient quantities to support natural reproduction; fertilized eggs must be reared in hatcheries and treated with supplemental thiamine. We evaluated transcriptional responses (via RNA sequencing) to thiamine treatment across families and found 3,616 genes differentially expressed between control (no supplemental thiamine) and treatment individuals. Fewer genes changed expression equally across families (i.e., additively) than exhibited genotype × environment interactions in response to thiamine. Differentially expressed genes were related to known physiological effects of thiamine deficiency, including oxidative stress, cardiovascular irregularities and neurological abnormalities. We also identified 1,446 putatively adaptive genes that were strongly associated with among‐family survival in the absence of thiamine treatment, many of which related to neurogenesis and visual perception. Our results highlight the utility of coupling RNA sequencing with formal survival analyses to identify candidate genes that underlie the among‐family variation in survival required for an adaptive response to natural selection.

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SalmoBase: an integrated molecular data resource for Salmonid species

Cited by 51 publications

References 7 publications

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

Extensive genetic differentiation between recently evolved sympatric Arctic charr morphs

Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs

Among‐family variation in survival and gene expression uncovers adaptive genetic variation in a threatened fish

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