Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Small RNA transcriptome in the Squalius alburnoides complex

ABSTRACT: 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).

ORGANISM(S): Squalius alburnoides

SUBMITTER: Angela InÃ¡cio

PROVIDER: E-GEOD-38691 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides.

Inácio Angela A Pinho Joana J Pereira Patrícia Matos PM Comai Luca L Coelho Maria Manuela MM

PloS one 20120718 7

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 showed that in response to the increase in genome dosage, triploids hybrids could regulate gene expression to a diploid state. In this ...[more]

PMID: 22815952

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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.

Project description:Current commercially available feeds for salmon are predominantly made of plant ingredients, with consequent changes to the composition and contents of a range of nutrients and other components in the diet. There are concerns that, with these major changes in raw materials, new feeds will affect not only the composition and contents of nutrients, but also the bioavailability and, combined with the limited knowledge of micronutrient requirements for Atlantic salmon, this might impact growth performance and health of the fish. The present study investigated the effects of graded levels of a micronutrient package supplemented to feeds formulated with low levels of marine ingredients and fed to diploid and triploid Atlantic salmon throughout the freshwater phase. Specifically, fish were fed three diets containing low levels of FM and FO and identical in formulation other than being supplemented with 3 levels (L1, 100 %; L2, 200 % and L3, 400 %) of a micronutrient mix formulated as a modification of current nutrient levels reported for salmon. Duplicate groups of diploid and triploid parr were fed the experimental diets from around 30 g to seawater transfer and the effects on growth performance, feed efficiency, biochemical composition, liver histology, hepatic gene expression (transcriptome) and smoltification efficiency determined. Microarray analysis revealed that the hepatic transcriptome profile of diploid fish fed diet L2 was more similar to that observed in triploids fed diet L3 than to those fed L2, suggesting that micronutrient requirements of triploid salmon may differ from levels accepted in diploid salmon. Different levels of micronutrient supplementation affected the expression of key genes involved in lipid metabolism. In particular sterol biosynthesis pathways (steroid and terpenoid backbone synthesis) were down-regulated in both L2-fed diploids and L3-fed triploids when compared with diet L1-fed diploids and triploids, respectively. Gene sets analysis showed an up-regulation of genes involved in immune processes in triploid salmon fed diet L3. Another biological category affected by diet in triploid salmon was genetic information processing. In fish fed diet L3 down-regulation of RNA degradation, proteasome, RNA polymerase, spliceosome and ribosome was observed, suggesting a decrease in protein turnover in this group, which may indicate a decrease in energy expenditure. In addition, one-carbon metabolism was affected by diet in diploid and triploid salmon.

Dataset Information

Small RNA transcriptome in the Squalius alburnoides complex

Publications

Global analysis of the small RNA transcriptome in different ploidies and genomic combinations of a vertebrate complex--the Squalius alburnoides.

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