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RNA-Seq provides insight to the body size evolution from comparative analyses of three Asia Sisoridae catfish

ABSTRACT: RNA-Seq provides insight to the body size evolution from comparative analyses of three Asia Sisoridae catfish

PROVIDER: PRJNA427776 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR6426010_1.fastq.gz	Fastqsanger.gz
	SRR6426010_2.fastq.gz	Fastqsanger.gz
	SRR6426020_1.fastq.gz	Fastqsanger.gz
	SRR6426020_2.fastq.gz	Fastqsanger.gz
	SRR6426030_1.fastq.gz	Fastqsanger.gz

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RNA-Seq provides insight to the body size evolution from comparative analyses of three Asia Sisoridae catfish

Project description:We sampled three catfishes from the Mekong River that belonging to the same Asia Sisoridae family but possessing extremely body size variations. We used RNA-Seq to compare the gene expression and sequence differences of these three sympatric species at their relatively early lives to search the possible genetic clues that equally response to growth. We found two crucial growth related candidate genes (AKT3 and SH2B1) were consistently up-regulated in BY when compared with both GM and OS at brain, liver and muscle respectively. The adaptor protein SH2B1 can bind to dozens of signaling molecules in response to a variety of extracellular growth signals, and the AKT3 can mediate a broad of intracellular cellular responses. The SH2B1 to AKT3 pathway could regulate growth, proliferation and biosynthetic processes at multiple levels through the AKT crosstalking effects, such as the overall enhancement of ribosome biogenesis we revealed from the multistep analyses strategy. Both the up-regulated DEGs and PSGs of BY converged to pyruvate metabolic process and cell cycle, which would also be critical for BY to accumulate cell growth and proliferation more actively to conduct the final big size. The different gene expression patterns would guide the further studies about body size evolution, and therelated candidate geneshighlighted in this study worth to be tested in the future.

2019-12-27 | GSE108597 | GEO

Transcriptome Analysis of Tra Catfish (Pangasianodon hypophthalmus) Early Development Provides Novel Insights for the Terrestrial Adaptation

Project description:Channel catfish (Ictalurus punctatus) and tra catfish (Pangasianodon hypophthalmus) both belong to the order Siluriformes. Channel catfish does not possess an air-breathing organ (ABO), and thus cannot breathe in the air, while tra catfish is a facultative air-breather and use the swim bladder as its air-breathing organ, which provides for aerial breathing in low oxygen conditions. Tra and channel catfish serve as a great comparative model for studying the transition of life from water to terrestrial living, as well as for understanding genes that are crucial for development of the swim bladder and the function of air-breathing in tra catfish. We selected seven developmental stages in tra catfish for RNA-Seq analysis based on their transition to a stage that could live at 0 ppm oxygen. More than 587 million sequencing clean reads were generated in tra catfish, and a total of 21, 448 unique genes were detected. A comparative genomic analysis was conducted between channel catfish and tra catfish. Gene expression analysis was performed for these tra catfish specific genes. Hypoxia challenge and microtomy experiments collectively suggested that there are critical timepoints for the development of the air-breathing function and swim bladder development stages in tra catfish. Key genes were identified to be the best candidates of genes related to the air-breathing ability in tra catfish. This study provides a large data resource for functional genomic studies in air-breathing function in tra catfish, and sheds light on the adaption of aquatic organisms to the terrestrial environment.

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Xenopus hybrids provide insight into cell and organism size control

Project description:Xenopus hybrids provide insight into cell and organism size control

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Transcriptome analysis revealed potential mechanisms of channel catfish growth advantage over blue catfish in tank culture environment

Project description:Channel catfish and blue catfish represent two economically important freshwater aquaculture species in the United States. Our study aims to investigate the gene expression differences between these two catfish species by high-throughput RNA sequencing to understand their associated phenotypic differences in growth and disease resistant. Our transcriptomic analyses provide some insights into gene function differences between the two species and the molecular basis of channel catfish growth advantage in the tank culture environment.

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Environmental dependent heterosis and transgressive gene expression in reciprocal hybrids between the channel catfish Ictalurus punctatus and the blue catfish Ictalurus furcatus

Project description:The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40-80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1,140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent hetero-sis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility.

2022-01-05 | GSE186603 | GEO

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Project description:Affymetrix single nucleotide polymorphism (SNP) array data were collected to study genome-wide patterns of genomic variation across a broad geographical range of Island Southeast Asian populations. This region has experienced an extremely complex admixture history. Initially settled ~50,000 years ago, Island Southeast Asia has since been the recipient of multiple waves of population movements, most recently by Austronesian-speaking groups ultimately from Neolithic mainland Asia and later arrivals during the historic era from India and the Middle East. We have genotyped SNPs in ~500 individuals from 30 populations spanning this entire geographical region, from communities close to mainland Asia through to New Guinea. Particular attention has been paid to genomic data that are informative for population history, including the role of recent arrivals during the historic era and admixture with archaic hominins.

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Expression analysis of Edwardsiella ictaluri 93-146 wild type and mutant strains during catfish fry encounter.

Project description:Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for host encounter. 4-plex NimbleGen array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri encountered with or without catfish fry. Each treatment had four biological replica and each plex had two probe sets.

2013-12-15 | E-GEOD-46007 | biostudies-arrayexpress

Expression analysis of Edwardsiella ictaluri 93-146 wild type and mutant strains during catfish serum exposure.

Project description:Edwardsiella ictaluri is the causitive agent of enteric septicemia of catfish, one of the most important diseases impacting US catfish industry. The overall objective of this study is to identify E. ictaluri genes required for serum resistance. 4-plex array study using total RNA obtained from wild type and mutant Edwardsiella ictaluri exposed to heat-inactivated catfish serum and normal serum. Each treatment had four biological replica and each plex had two probe sets.

2013-12-15 | E-GEOD-46011 | biostudies-arrayexpress

Transcriptome analysis reveals key gene expression changes in blue catfish sperm in response to cryopreservation

Project description:Cryopreservation of blue catfish sperm can cause variable embryo hatch rates, which is the limiting factor for hybrid catfish breeding. In this study, we investigated gene expression changes caused by cryopreservation using transcriptome profiles of fresh sperm samples and cryopreserved sperm from the same set of blue catfish.

2022-06-26 | GSE204687 | GEO

Xenopus hybrids provide insight into cell and organism size control

Project description:Determining how size is controlled is a fundamental question in biology that is poorly understood at the organismal, cellular and subcellular levels. The Xenopus species, X. laevis and X. tropicalis differ in size at all three of these levels. Despite these differences, fertilization of X. laevis eggs with X. tropicalis sperm gives rise to viable hybrid animals that are intermediate in size. Hybrid and X. laevis embryos initially start from the same size egg and develop at the same rate, but hybrid animals were smaller by the tailbud stage, and reduced nuclear to cell size ratios were observed shortly after zygotic genome activation (ZGA), indicating that differential gene expression may contribute to size differences. Transcriptome analysis at the onset of ZGA identified twelve transcription factors paternally expressed in hybrids. A screen of these X. tropicalis factors by expression in X. laevis embryos revealed that Hes7 and Ventx2 were sufficient to significantly reduce X. laevis organismal size by the tailbud stage, although nuclear to cell size ratios were not significantly affected. Together, these results suggest that transcriptional regulation contributes to biological size control in Xenopus.

2018-12-19 | GSE118382 | GEO

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