Taming of the wild: a new tool for cross study RNA-seq analysis applied to behavioural traits in dogs and tame foxes
Creators: name: Lobo, Diana
name: Godinho, Raquel
name: Archer, John
Publisher: name: Zenodo
Year: 2022

description: <strong>Conference Details: </strong> 8th European Congress of Mammalogy, 23 - 27 September 2019, Warsaw (url) This talk is based on a paper titled "<em>On taming the effect of transcript level intra-condition count variation during differential expression analysis: a story of dogs, foxes and wolves</em>" that is available here. Presented by Diana Lobo. <strong>Abstract</strong> Animal domestication has led to a shared spectrum of behavioral changes, including taming. Patterns of gene expression in the brain of domestic animals may answer if tameness is controlled by a common set of genes. The evolution of RNA-Seq has yielded archived datasets that posse the potential for providing an unprecedented inter-study insight into transcriptome evolution, once background noise has been reduced. In this study, we present a method to quantify intra-condition variation and to remove reference-based transcripts that are associated with highly variable read counts, prior to differential expression analysis. As a case study, we demonstrate our approach at both inter and intra-study levels using RNA-seq data from brain samples of dogs, wolves and foxes (aggressive and tame) in order to identify common genes associated with tame behavior. We explored several levels of filter thresholds based on intra-condition variation and perform subsequent differential expression analysis between wolves vs dogs and aggressive vs tame foxes. By applying our method, the distribution of the gene-wise dispersion estimates improved and the number of outliers detected in differential expression analysis decreased. Several genes that were initially considered as differentially expressed in the non-filtered datasets were associated with high intra-condition variation and thus removed. Additionally, by optimizing the detection of differentially expressed transcripts, the overall number increased between dogs vs wolves and tame vs aggressive foxes when compared to the non-filtered datasets. The expression analysis revealed 21 over expressed and 3 under expressed gene families in common in the brain of dogs and tame foxes. Among those, seven and one individual genes were in common over and under expressed, respectively, to dogs and tame foxes. These candidates include genes involved in brain development, neurotransmission and immune response, functions known to be associated with domestication. The method is freely available at: https://sourceforge.net/projects/tvscript/. Related software to this project are:<br> 1. CStone <br> 2. CSReadGen<br> 3. CView<br> 4. ChimSim <br> 5. TVScript &lt; General details of the supporting projects are available here (wolf hybridization) and here (removal of chimeras).
description: This work was supported by the Portuguese Foundation for Science and Technology, FCT, projects PTDC/BIA-EVF/2460/2014 and PTDC/BIA-EVL/29115/2017. DL, RG were supported by FCT (PD/BD/132403/2017 to DL, contract under DL57/2016 to RG) and JA was supported by Funds through FCT under the references POCI-01-0145-FEDER-029115 and PTDC/BIA-EVL/29115/2017.