Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids

Abstract

The detection of external and internal cues alters gene expression in the brain which in turn may affect neural networks that underly behavioral responses. Previous studies have shown that gene expression profiles differ between major brain regions within individuals and between species with different morphologies, cognitive abilities and/or behaviors. A detailed description of gene expression in all macroanatomical brain regions and in species with similar morphologies and behaviors is however lacking. Here, we dissected the brain of two cichlid species into six macroanatomical regions. Ophthalmotilapia nasuta and O. ventralis have similar morphology and behavior and occasionally hybridize in the wild. We use 3′ mRNA sequencing and a stage-wise statistical testing procedure to identify differential gene expression between females that were kept in a social setting with other females. Our results show that gene expression differs substantially between all six brain parts within species: out of 11,577 assessed genes, 8,748 are differentially expressed (DE) in at least one brain part compared to the average expression of the other brain parts. At most 16% of these DE genes have |log2FC| significantly higher than two. Functional differences between brain parts were consistent between species. The majority (61–79%) of genes that are DE in a particular brain part were shared between both species. Only 32 genes show significant differences in fold change across brain parts between species. These genes are mainly linked to transport, transmembrane transport, transcription (and its regulation) and signal transduction. Moreover, statistical equivalence testing reveals that within each comparison, on average 89% of the genes show an equivalent fold change between both species. The pronounced differences in gene expression between brain parts and the conserved patterns between closely related species with similar morphologies and behavior suggest that unraveling the interactions between genes and behavior will benefit from neurogenomic profiling of distinct brain regions.

Early neurogenomic response associated with variation in guppy female mate preference

“…Only eight genes were differentially expressed in both tissues. This low overlap is not surprising considering the demonstrated differences in the expression of activity-regulated genes across brain regions in birds and fish10,39. Even though evolutionary models predict sex linkage of female preference genes under the good genes model40,41, we did not observe an enrichment of these candidate genes on the X chromosome (LG12, P>0.05).…”

Gene expression in the social behavior network of the wire‐tailed manakin (Pipra filicauda) brain

“…[31][32][33] Mounting evidence suggests, however, that patterns of gene expression vary among subdivisions of the vertebrate brain. [34][35][36][37] For example, studies of birds and mammals have showed distinctive gene expression profiles in the amygdala and hypothalamus, [38][39][40] suggesting that suites of behaviorally relevant genes are differentially expressed among nodes of the SBN. Indeed, results from candidate gene studies have showed that expression levels of key neuroendocrine genes can vary widely across regions of the SBN and that relationships between neuroendocrine gene expression and behavior are region-dependent.…”

“…To date, a number of studies have leveraged whole‐brain transcriptomic data to identify the gene expression profiles associated with sex, social status, ecotype and reproductive strategy within species, as well as interspecific differences in reproductive and social behaviors across species . Mounting evidence suggests, however, that patterns of gene expression vary among subdivisions of the vertebrate brain . For example, studies of birds and mammals have showed distinctive gene expression profiles in the amygdala and hypothalamus, suggesting that suites of behaviorally relevant genes are differentially expressed among nodes of the SBN.…”