Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs
- Published
- Accepted
- Subject Areas
- Developmental Biology, Ecology, Evolutionary Studies, Genomics, Freshwater Biology
- Keywords
- Divergence, Salmonid, Transcriptome, Evolution, Lake Thingvallavatn, Salvelinus alpinus, 3'-bias, RNA sequencing
- Copyright
- © 2017 Guðbrandsson et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs. PeerJ Preprints 5:e3318v1 https://doi.org/10.7287/peerj.preprints.3318v1
Abstract
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.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
The results of gene ontology analyses of the transcripts with significant expression difference between morphs (or morph by time interaction) in the Arctic charr developmental transcriptome. The enrichment was tested for transcripts and genes (SalmoBase)
GO.ID: Identification number for Gene Ontology categories
Term: The Gene Ontology term or description of the category
numDE.t: Number of transcripts within expression cluster in each GO-category
numIn.t: Total number of transcripts in each GO-category
fdr.t: Multiple testing corrected P-value (FDR) for enrichment based on transcripts
p.t: Uncorrected P-value for enrichment based on transcripts
numDE.g: Number of genes (SalmoBase) within expression cluster in each GO-category
numIn.g: Total number of genes (SalmoBase) in each GO-category
fdr.g: Multiple testing corrected P-value (FDR) for enrichment based on genes
p.g: Uncorrected P-value for enrichment based on genes
Cluster: Expression cluster
GOclust: Super-GO-categories based on categories semantic similarity (see Methods)
Information about genes used in qPCR. Detailed gene names, primer sequence, amplicon size and transcripts in the assembly used for comparison
Gene Symbol: The symbol or short gene name used in figures and text
Description: Full name of each gene
Forward primer: Sequence for the forward qPCR primer in 5’-3’ orientation
Reverse primer: Sequence for the reverse qPCR primer in 5’-3’ orientation
Amplicon size: Size of the sequence amplified in the qPCR reaction
Transcripts: The id of assembled transcripts in the transciptome that the primers bind to and were used for comparison of expression. If there are more than one transcipts for each gene the ids are separated by a semicolon.