Data from: Regulatory genome annotation for 33 insect species

Annotation of newly-sequenced genomes frequently includes genes, but
rarely covers important non-coding genomic features such as the cis
-regulatory modules—e.g., enhancers and silencers—that regulate gene
expression. Here, we begin to remedy this situation by developing a
workflow for rapid initial annotation of insect regulatory sequences, and
provide a searchable database resource with enhancer predictions for 33
genomes. Using our previously-developed SCRMshaw computational enhancer
prediction method, we predict over 2.8 million regulatory sequences along
with the tissues where they are expected to be active, in a set of insect
species ranging over 360 million years of evolution. Extensive analysis
and validation of the data provides several lines of evidence suggesting
that we achieve a high true-positive rate for enhancer prediction. One, we
show that our predictions target specific loci, rather than random genomic
locations. Two, we predict enhancers in orthologous loci across a diverged
set of species to a significantly higher degree than random expectation
would allow. Three, we demonstrate that our predictions are highly
enriched for regions of accessible chromatin. Four, we achieve a
validation rate in excess of 70% using in vivo reporter gene assays. As we
continue to annotate both new tissues and new species, our regulatory
annotation resource will provide a rich source of data for the research
community and will have utility for both small-scale (single gene, single
species) and large-scale (many genes, many species) studies of gene
regulation. In particular, the ability to search for functionally-related
regulatory elements in orthologous loci should greatly facilitate studies
of enhancer evolution even among distantly related species.