Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids
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 differe...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2018-03-01
|
| Series: | Frontiers in Neuroscience |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fnins.2018.00136/full |
| _version_ | 1818494145650491392 |
|---|---|
| author | Sofie Derycke Sofie Derycke Loic Kéver Loic Kéver Koen Herten Koen Van den Berge Koen Van den Berge Maarten Van Steenberge Maarten Van Steenberge Jeroen Van Houdt Lieven Clement Lieven Clement Pascal Poncin Eric Parmentier Erik Verheyen |
| author_facet | Sofie Derycke Sofie Derycke Loic Kéver Loic Kéver Koen Herten Koen Van den Berge Koen Van den Berge Maarten Van Steenberge Maarten Van Steenberge Jeroen Van Houdt Lieven Clement Lieven Clement Pascal Poncin Eric Parmentier Erik Verheyen |
| author_sort | Sofie Derycke |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-10T18:02:42Z |
| format | Article |
| id | doaj.art-f4eacbc8226740a194de4caa30b7f82c |
| institution | Directory Open Access Journal |
| issn | 1662-453X |
| language | English |
| last_indexed | 2024-12-10T18:02:42Z |
| publishDate | 2018-03-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Neuroscience |
| spelling | doaj.art-f4eacbc8226740a194de4caa30b7f82c2022-12-22T01:38:43ZengFrontiers Media S.A.Frontiers in Neuroscience1662-453X2018-03-011210.3389/fnins.2018.00136302361Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia CichlidsSofie Derycke0Sofie Derycke1Loic Kéver2Loic Kéver3Koen Herten4Koen Van den Berge5Koen Van den Berge6Maarten Van Steenberge7Maarten Van Steenberge8Jeroen Van Houdt9Lieven Clement10Lieven Clement11Pascal Poncin12Eric Parmentier13Erik Verheyen14Operational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, BelgiumDepartment of Biology, Ghent University, Ghent, BelgiumLaboratory of Functional and Evolutionary Morphology, University of Liège, Liège, BelgiumBehavioural Biology Unit, Ethology and Animal Psychology, University of Liège, Liège, BelgiumDepartment of Human Genetics, Genomics Core Facility, KU Leuven, Leuven, BelgiumDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, BelgiumBioinformatics Institute Ghent, Ghent University, Ghent, BelgiumOperational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, BelgiumSection Vertebrates, Ichthyology, Royal Museum for Central Africa, Tervuren, BelgiumDepartment of Human Genetics, Genomics Core Facility, KU Leuven, Leuven, BelgiumDepartment of Applied Mathematics, Computer Science and Statistics, Ghent University, Ghent, BelgiumBioinformatics Institute Ghent, Ghent University, Ghent, BelgiumBehavioural Biology Unit, Ethology and Animal Psychology, University of Liège, Liège, BelgiumLaboratory of Functional and Evolutionary Morphology, University of Liège, Liège, BelgiumOperational Direction Taxonomy and Phylogeny, Royal Belgian Institute for Natural Sciences, Brussels, BelgiumThe 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.http://journal.frontiersin.org/article/10.3389/fnins.2018.00136/fullcerebellumsocial behaviorcichlid fishequivalence testinggene-level FDRneurogenomics |
| spellingShingle | Sofie Derycke Sofie Derycke Loic Kéver Loic Kéver Koen Herten Koen Van den Berge Koen Van den Berge Maarten Van Steenberge Maarten Van Steenberge Jeroen Van Houdt Lieven Clement Lieven Clement Pascal Poncin Eric Parmentier Erik Verheyen Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids Frontiers in Neuroscience cerebellum social behavior cichlid fish equivalence testing gene-level FDR neurogenomics |
| title | Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids |
| title_full | Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids |
| title_fullStr | Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids |
| title_full_unstemmed | Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids |
| title_short | Neurogenomic Profiling Reveals Distinct Gene Expression Profiles Between Brain Parts That Are Consistent in Ophthalmotilapia Cichlids |
| title_sort | neurogenomic profiling reveals distinct gene expression profiles between brain parts that are consistent in ophthalmotilapia cichlids |
| topic | cerebellum social behavior cichlid fish equivalence testing gene-level FDR neurogenomics |
| url | http://journal.frontiersin.org/article/10.3389/fnins.2018.00136/full |
| work_keys_str_mv | AT sofiederycke neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT sofiederycke neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT loickever neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT loickever neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT koenherten neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT koenvandenberge neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT koenvandenberge neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT maartenvansteenberge neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT maartenvansteenberge neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT jeroenvanhoudt neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT lievenclement neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT lievenclement neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT pascalponcin neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT ericparmentier neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids AT erikverheyen neurogenomicprofilingrevealsdistinctgeneexpressionprofilesbetweenbrainpartsthatareconsistentinophthalmotilapiacichlids |