Centre for Integrative Genetics (CIGENE), Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK.
BMC Genomics. 2019 Sep 2;20(1):694. doi: 10.1186/s12864-019-6051-0.
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.
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.
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 .
最近在鲑鱼鱼类中开发的基因组资源为研究基础广泛的特性的基因组学提供了工具，包括野生生命史性状变异、水产养殖中的经济重要性状以及全基因组加倍的进化后果。尽管现在已经为一些鲑鱼物种建立了基因组组装，但缺乏调节注释阻碍了我们对非编码调节区域的遗传变异如何影响基因表达和下游表型效应的机制理解。
我们提出了 SalMotifDB，这是一个数据库以及用于分析五个鲑鱼基因组中转录因子（TFs）及其顺式调节结合位点的相关网络和 R 接口。SalMotifDB 整合了来自大量后生动物 motif 数据库的 3072 个非冗余 DNA 模式（基序）的 TF 结合位点信息。通过基序匹配和 TF 预测，我们使用这些多物种数据库构建了鲑鱼物种中的假定调控网络。SalMotifDB 的实用性通过以下方式得到证明：表明关键脂质代谢调节剂被预测调节一组受饲料中不同脂质和脂肪酸含量影响的基因，并表明我们的基序数据库解释了源自鲑鱼特异性全基因组加倍的基因重复的基因表达差异的很大一部分。
SalMotifDB 是分析鲑鱼物种中转录因子、它们的结合位点和由此产生的基因调控网络的有效工具，并且将成为更好地理解鲑鱼基因调控和相关表型的机制的重要工具。SalMotifDB 可在 https://salmobase.org/apps/SalMotifDB 上获得。
