Small RNA transcriptome in the Squalius alburnoides complex
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ABSTRACT:
PROVIDER: PRJNA169558 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR517904.fastq.gz | Fastqsanger.gz | |||
| SRR517905.fastq.gz | Fastqsanger.gz | |||
| SRR517906.fastq.gz | Fastqsanger.gz | |||
| SRR517907.fastq.gz | Fastqsanger.gz |
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Project description:The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.
2013-01-02 | GSE38691 | GEO
Project description:The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change. 4 samples were analyzed corresponding to 4 genomic constitutions: PAA, PA, AA and PP. For each sample, a library based on 3 individuals of the same genomic constitution was prepared. From each individual, 3 types of tissues were collected for RNA extraction (brain, liver and muscle).
2013-01-02 | E-GEOD-38691 | biostudies-arrayexpress
Project description:miRNA expression profile and small RNA transcriptome in the Squalius alburnoides complex
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Project description:The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.
2013-01-02 | GSE36894 | GEO
Project description:miRNA expression profile in the Squalius alburnoides complex
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Project description:The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. In this complex, the constant switch of the genome composition in consecutive generations, very frequently involving a change on the ploidy level, promotes repetitive situations of potential genomic shock. Previously in this complex, it was shown that in response to the increase in the genome dosage, triploid hybrids could regulate gene expression to a diploid state. In this work, we compared the small RNA profiles in the different genomic compositions interacting in the complex. Using high-throughput arrays and sequencing technologies, we were able to verify that diploid and triploid hybrids were closely related: they shared most of their sequences and their miRNA expression profiles were highly correlated. However, an overall view indicates an up-regulation of a substantial number of miRNAs in triploids. Also, the global miRNA expression in triploids was higher than predicted from an additive model. These results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change. In this study, miRNA expression from 3 adult tissues (brain, muscle and liver) from 3 individuals of each genomic composition (PAA, PA, AA and PP) was analysed using microarrays.
2013-01-02 | E-GEOD-36894 | biostudies-arrayexpress
Project description:How allopolyploids are able not only to cope but profit from their condition is a question that remain elusive, but of great importance within the wide context of successful hybrid polyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian S. alburnoides fish complex. Previously, based on the evaluation of 7 genes, it was reported that the transcription levels between diploid and triploid hybrid S. alburnoides were similar. If this phenomenon would occur on a full genomic scale, a wide functional diploidization could be related to the success of polyploids. We generated RNA-seq data from whole juvenile fish and from an adult tissue, to perform the first comparative quantitative transcriptomic analysis between ploidy levels of a vertebrate allopolyploid. We found 64% in juvenilesM-b full body samples and 44% in liver samples of similar expression between diploid and triploid hybrids, and those genes are mostly involved in processes of basal biological maintenance of the cells. Yet, respectively only 29% and 15% of transcripts presented accurate dosage compensation. Therefore, an exact functional diploidization of the triploid genome does not occur, but globally a significant down regulation of gene expression in triploids was observed. We find that for those genes which show similar expression levels in diploids and triploids, expression in triploids is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative flexibility of expression may be a strong contributor to overcome the 'genomic shock', and be an immediate evolutionary advantage of allopolyploids. Genotypes: Squalius alburnoides is an allopolyploid cyprinid, resulting from interspecific hybridization between females of Squalius pyrenaicus (P genome) and males of a now extinct species related to Anaecypris hispanica (A genome). S. alburnoides natural populations arecomposed of animals of different ploidy levels and genomic constitutions (different genotypes). The predominant S. alburnoides complex intervenients in the Iberian Peninsula southern rivers are the hybrid triploid PAA, diploid PA, the parental-like diploid AA and the parental species S. pyrenaicus PP.
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