SalMotifDB: a tool for analyzing putative transcription factor binding sites in salmonid genomes

Abstract

Background Recently developed genome resources in Salmonid fish provides tools for studying the genomics underlying a wide range of properties including life history trait variation in the wild, economically important traits in aquaculture and the evolutionary consequences of whole genome duplications. Although genome assemblies now exist for a number of salmonid species, the lack of regulatory annotations are holding back our mechanistic understanding of how genetic variation in non-coding regulatory regions affect gene expression and the downstream phenotypic effects. Results We present SalMotifDB, a database and associated web and R interface for the analysis of transcription factors (TFs) and their cis -regulatory binding sites in five salmonid genomes. SalMotifDB integrates TF-binding site information for 3072 non-redundant DNA patterns (motifs) assembled from a large number of metazoan motif databases. Through motif matching and TF prediction, we have used these multi-species databases to construct putative regulatory networks in salmonid species. The utility of SalMotifDB is demonstrated by showing that key lipid metabolism regulators are predicted to regulate a set of genes affected by different lipid and fatty acid content in the feed, and by showing that our motif database explains a significant proportion of gene expression divergence in gene duplicates originating from the salmonid specific whole genome duplication. Conclusions SalMotifDB is an effective tool for analyzing transcription factors, their binding sites and the resulting gene regulatory networks in salmonid species, and will be an important tool for gaining a better mechanistic understanding of gene regulation and the associated phenotypes in salmonids. SalMotifDB is available at https://salmobase.org/apps/SalMotifDB . Electronic supplementary material The online version of this article (10.1186/s12864-019-6051-0) contains supplementary material, which is available to authorized users.

Comparative transcriptomics reveals domestication‐associated features of Atlantic salmon lipid metabolism

“…Significant values ( p < .05) were generated based on a hypergeometric test where the number of DEGs was compared to total genes annotated to each KO term. A test for enrichments of transcription factor binding site (TFBS) motifs in the promoter regions (between −1,000 and 100 bp from the transcription start site) of salmon genes was done by using a hypergeometric test in the R package salmotifdb , which interacts with a database of TFBSs for salmonids (https://salmobase.org/apps/SalMotifDB) (Mulugeta et al., 2019).…”

Diversified regulation of circadian clock gene expression following whole genome duplication

“…Heatmaps were generated in R using custom scripts for pheatmap. Transcription factor binding site analysis was conducted using SalmotifDB [37]. qPCR cDNA was synthesised from sample total RNA using high capacity RNA to cDNA kit (Applied Biosystems).…”

Photoperiod-dependent developmental reprogramming of the transcriptional response to seawater entry in Atlantic salmon (Salmo salar)

“…We used MotifDb ((Mulugeta et al, 2019) (https://salmobase.org/apps/SalMotifDB/) to determine how NFAT response elements are associated with SW-induced changes in gene expression (fig. 4A), focusing on changes occurring at the last sampling point (T6, day 110) of the experiment.…”

“…Motif enrichment analysis was performed using SalMotifDB-shiny tool (https://cigene.no/tools/) (Mulugeta et al, 2019). This tool accesses a database containing over 19,000 predicted transcription factor binding sites (TFBSs) found in the proximal promoter regions (−1,000/+200bp from TSS) of salmonid genes.…”