Comparison of embryonic expression within multigene families using the flyexpress discovery platform reveals more spatial than temporal divergence

Abstract

Overlaps in spatial patterns of gene expression are frequently an initial clue to genetic interactions during embryonic development. However, manual inspection of images requires considerable time and resources impeding the discovery of important interactions because tens of thousands of images exist. The FlyExpress discovery platform was developed to facilitate data-driven comparative analysis of expression pattern images from Drosophila embryos. An image-based search of the BDGP and Fly-FISH datasets conducted in FlyExpress yields fewer but more precise results than text-based searching when the specific goal is to find genes with overlapping expression patterns. We also provide an example of a FlyExpress contribution to scientific discovery: an analysis of gene expression patterns for multigene family members revealed that spatial divergence is far more frequent than temporal divergence, especially after the maternal to zygotic transition. This discovery provides a new clue to molecular mechanisms whereby duplicated genes acquire novel functions.

In locusanalysis of patterning evolution in the BMPR2 Wishful thinking

“…One way to identify common mechanisms of gene regulation is to search for overlapping spatiotemporal expression domains (Konikoff et al, 2012;Kumar et al, 2017). In D. melanogaster, the anterior domain of the follicular epithelium is patterned by BMP signaling (Twombly et al, 1996).…”

Functional genetic characterization of salivary gland development in Aedes aegypti

“…A number of D. melanogaster salivary gland marker genes were selected through literature and FlyExpress ontology [21,22] searches. Expression of the mosquito orthologs of these genes (Additional file 1), which were predicted to function as mosquito salivary gland markers, was assessed during Ae.…”

“…aegypti embryogenesis. At the onset of these studies, RNA expression patterns of crebA and PAPS synthetase ( paps ), which function as both early and late markers of the developing D. melanogaster salivary gland [16,21,22], were analyzed in detail at multiple embryonic stages of Ae. aegypti development.…”

“…A full list of these genes, including their putative functions and their orthology relationships with respect to the Drosophila genes, is provided in Additional file 1. Analysis of the expression of these additional markers, including mosquito orthologs of several genes that are expressed in the D. melanogaster VNE placodes ( sage , sec63 , syx18 and TRAM ) [21,22], provided further confirmation that the Ae. aegypti salivary gland rudiments do not reside in the VNE.…”

“…Candidate marker genes were selected on the basis of their orthology to known salivary gland markers in D. melanogaster, which were selected through literature searches and by using the ontology search tool in FlyExpress [21,22]. Orthology calls were prepared with the aid of Biomart [23] and VectorBase [24].…”