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

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Congrats @CharrVein Differential gene expr. during development in recently evolved & sympatric Arctic charr morphs https://t.co/lVTqYXT0XG
RT @vonStadarhraun: Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
RT @vonStadarhraun: Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
RT @vonStadarhraun: Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
RT @speciation_pubs: peerJ: Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs htt…
RT @CharrVein: Dev. expression of sympatric Arctic charr morphs https://t.co/IiUCodszyf via @PeerJPreprints by the fab Johannes @vonStadarh…
Dev. expression of sympatric Arctic charr morphs https://t.co/IiUCodszyf via @PeerJPreprints by the fab Johannes @vonStadarhraun
RT @vonStadarhraun: Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs https://t.co/x1bneWMgPP …
46 days ago
Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs https://t.co/65xO4r32ek
peerJ: Differential gene expression during early development in recently evolved and sympatric Arctic charr morphs https://t.co/r7ZGwVum9W
RT @vonStadarhraun: Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
Our latest preprint on gene expression in Arctic charr https://t.co/mUIx6XLK0T
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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)

DOI: 10.7287/peerj.preprints.3318v1/supp-1

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.

DOI: 10.7287/peerj.preprints.3318v1/supp-2

Additional Information

Competing Interests

The authors declare that they have no competing interests.

Author Contributions

Jóhannes Guðbrandsson conceived and designed the experiments, performed the experiments, analyzed the data, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Sigríður Rut Franzdóttir conceived and designed the experiments, performed the experiments, wrote the paper, reviewed drafts of the paper.

Bjarni Kristófer Kristjánsson performed the experiments, contributed reagents/materials/analysis tools, reviewed drafts of the paper.

Ehsan Pashay Ahi performed the experiments, analyzed the data, prepared figures and/or tables, reviewed drafts of the paper.

Valerie Helene Maier performed the experiments, reviewed drafts of the paper.

Sigurður Sveinn Snorrason conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Zophonías Oddur Jónsson conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Arnar Pálsson conceived and designed the experiments, performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

Ethics committee approval is not needed for regular or scientific fishing in Iceland (The Icelandic law on Animal protection, Law 15/1994,

last updated with Law 55/2013).

Sampling of embryos for RNA extraction was performed by Holar University College Aquaculture

Research Station (HUC-ARC) personnel.

HUC-ARC has an operational license according to Icelandic law

on aquaculture (Law 71/2008), which includes clauses of best practices for animal care and experiments.

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

Fishing was performed with the permissions both from the owner of the

land in Mjóanes and from the Thingvellir National Park commission.

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

The sequencing reads from the 48 samples were deposited into the

NCBI SRA archive under BioProject identifier PRJNA391695 and with accession numbers: SRS2316381

to SRS2316428

Data Deposition

The following information was supplied regarding data availability:

Figshare

doi:10.6084/m9.figshare.5445610

https://figshare.com/s/22cc482d577aad7bc125

Funding

The project was funded by The Icelandic Center for Research (grant number: 100204011) to SSS, AP, ZOJ and BKK, The University of Iceland Doctoral Fund to JG and University of Iceland research fund to AP, SSS and ZOJ. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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