Ontology highlight
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PROVIDER: PRJNA1041468 | ENA |
REPOSITORIES: ENA
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Project description:Electric fishes have independently evolved six times. Most of these fish are weakly electric and they use their discharge mainly for orientation and communication. In the African weakly electric fish genus Campylomormyrus, electric organ discharge (EOD) signals are strikingly different in shape and duration among closely related species, they contribute to pre-zygotic isolation and may have triggered an adaptive radiation. We performed mRNA sequencing on electric organs (EOs) and skeletal muscle (SMs; from which the EOs derive) from three species with short (0.4 ms), medium (5 ms), and long (40 ms) EODs and two different cross-species hybrids. Using pairwise comparison of differential gene expression between EOs and SMs, we identified 1,444 up regulated genes in EO shared by all five species/hybrids cohorts, rendering them candidate genes for EO-specific properties in Campylomormyrus. To understand how gene expression contributes to the variation in EOD duration, we made cross species comparisons among species and tissue. We identified three types of EOD-duration-related expression patterns and several candidate genes, including KCNJ2, KLF5 and SLC24a2, their upregulation may contribute to increased EOD duration, along with a down-regulated gene KCNK6. Hybrids between a short (C. compressirostris) and a long (C. rhynchophorus) discharging species exhibit EODs of intermediate duration and showed imbalanced expression of KCNJ2 alleles. The preferential expression of the C. rhynchophorus allele is in line with a higher expression level in that parental species and points towards a cis-regulatory difference at this locus, relative to EOD duration. A further candidate gene, KLF5, is a transcription factor potentially balancing potassium channel gene expression, a crucial process for the formation of an EOD. Unraveling the genetic basis of the species-specific modulation of the EOD in Campylomormyrus is crucial for understanding the adaptive radiation of this emerging model taxon of ecological (perhaps even sympatric) speciation.
2023-08-31 | GSE240783 | GEO
Project description:Hybridization can act as a catalyst for rapid phenotypic evolution by introducing novel allelic combinations, which can affect hybrid phenotype through changes in gene expression. The African weakly electric fish use their muscle-derived electric organ to produce electric organ discharge (EOD) for electrocommunication and electrolocation. The EOD in genus Campylomormyrus and cross-species hybrids is usually species-specific and varies during ontogeny. We compared the gene expression patterns and allele specific expression between juvenile and adult individuals in C. compressirostris (EOD duration 0.4 ms in juvenile and 0.4 ms in adult), C. rhynchophorus (EOD duration 5 ms in juvenile and 40 ms in adult) and their hybrid (EOD duration 0.4 ms in juvenile and 4 ms in adult). Differentially expressed genes between juveniles and adults were highly enriched in “membrane”, “plasma membrane” and “cytoplasm” Go Ontogeny terms. We detected several potassium channel-related genes (e.g. KCNJ2, ADCYAP1) that are potentially involved in the EOD development during ontogeny. The alleles from C. compressirostris show dominant expression in the hybrid at juvenile and adult life stages. KCNJ2 is the only gene that exhibits allelic dominance of C. rhynchophorus allele, and has an increasing expression during ontogeny in this allele. This suggests that the EOD development in hybrids could be related to the increasing allelic expression of the C. rhynchophorus allele under the scenario of overall dominance of C. compressirostris alleles. Our study sheds light in the evolution of the electric organ discharge in electric fishes and on the role of introgressive hybridization in complex phenotypic traits.
2023-08-31 | GSE240784 | GEO
Project description:Gene and allele specific expression during electric organ ontogeny in African weakly electric fish and hybrid
| PRJNA1005245 | ENA
Project description:Pacbio genome sequencing of the African weakly electric fish was performed and assembed with Hifiasm assembler
| PRJEB45430 | ENA
Project description:We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish. for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout 32 samples
2008-09-01 | E-GEOD-12031 | biostudies-arrayexpress
Project description:We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al.,Am J Physiol Regul Integr Comp Physiol 294: R1154–R1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual liver of these fish. for each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. Keywords: Nutritional genomics, response to divergent selection for muscle fattening, liver metabolism, rainbow trout
2008-09-01 | GSE12031 | GEO
Project description:The brown ghost knifefish (Apteronotus leptorhynchus) is a weakly electric teleost fish of particular interest as a model organism for a variety of research areas in neuroscience, including neurophysiology, neuroethology, and neurobiology. This versatile model system has been more recently used in the study of central nervous system development and regeneration during adulthood, as well as in the study of vertebrate aging and senescence. Despite substantial scientific interest in this species, no genomic resources are currently available. After evaluating several trimming and transcript reconstruction strategies, de novo assembly using Trinity uncovered at least 11,847 unique components (“genes”) containing full or near-full length protein sequences based on alignment to a reference set of known Actinopterygii protein sequences, with as many as 42,459 components containing at least a partial protein-coding sequence, providing broad coverage of the proteome. Shotgun proteomics confirmed translation of open reading frames from over 2,000 transcripts, including alternative splice variants. Assignment of tandem mass spectra obtained was shown to be greatly improved with the assembly compared with using databases of sequences from closely related organisms.
2015-07-16 | PXD001285 | Pride
Project description:Comparative transcriptomic analysis: dietary treatment, genetic selection, and muscle fat content We used fish from two divergent lines of rainbow trout, selected for low or high muscle fat content (respectively L and F lines) and fed two different diets, containing either 10% (LE diet) or 23% (HE diet) lipids. For more details about experimental fish and diets, see Kolditz et al., Am J Physiol Regul Integr Comp Physiol 294: R1154âR1164, 2008. There are 4 experimental conditions: L-LE, L-HE, F-LE and F-HE. This experiment contain the data derived from the hybridization of the RNA extracted from individual muscle of these fish. For each membrane, spots with an oligonucleotide signal lower than three times the background level were excluded from the analysis. After this filtering step, signal processing was performed using the vector oligonucleotide data to correct each spot signal according to the actual amount of DNA present in each spot. After correction, the signal was normalized by dividing each gene expression value by the median value of the array. The study consisted of 19 samples total.
2010-05-15 | E-GEOD-16577 | biostudies-arrayexpress