Dataset Information

Gene expression dosage regulation in an allopolyploid fish.

ABSTRACT: How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full genomic scale, a wide functional ''diploidization'' could be related to the success of these polyploids. We generated RNA-seq data from whole juvenile fish and from adult livers, to perform the first comparative quantitative transcriptomic analysis between diploid and triploid individuals of a vertebrate allopolyploid. Together with an assay to estimate relative expression per cell, it was possible to infer the relative sizes of transcriptomes. This showed that diploid and triploid S. alburnoides hybrids have similar liver transcriptome sizes. This in turn made it valid to directly compare the S. alburnoides RNA-seq transcript data sets and obtain a profile of dosage responses across the S. alburnoides transcriptome. We found that 64% of transcripts in juveniles' samples and 44% in liver samples differed less than twofold between diploid and triploid hybrids (similar expression). Yet, respectively 29% and 15% of transcripts presented accurate dosage compensation (PAA/PA expression ratio of 1 instead of 1.5). Therefore, an exact functional diploidization of the triploid genome does not occur, but a significant down regulation of gene expression in triploids was observed. However, for those genes with similar expression levels between diploids and triploids, expression is not globally strictly proportional to gene dosage nor is it set to a perfect diploid level. This quantitative expression flexibility may be a strong contributor to overcome the genomic shock, and be an immediate evolutionary advantage of allopolyploids.

SUBMITTER: Matos I

PROVIDER: S-EPMC4366067 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature

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Gene expression dosage regulation in an allopolyploid fish.

Matos I I Machado M P MP Schartl M M Coelho M M MM

PloS one 20150319 3

How allopolyploids are able not only to cope but profit from their condition is a question that remains elusive, but is of great importance within the context of successful allopolyploid evolution. One outstanding example of successful allopolyploidy is the endemic Iberian cyprinid Squalius alburnoides. Previously, based on the evaluation of a few genes, it was reported that the transcription levels between diploid and triploid S. alburnoides were similar. If this phenomenon occurs on a full gen ...[more]

PMID: 25789776

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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:Allopolyploidization is accompanied by changes in gene expression that are thought to contribute to phenotypic diversification. Here we describe global changes in the single-celled cotton fiber proteome of two natural allopolyploid species (Gossypium hirsutum and G. barbadense) and living models of their diploid parents using two different proteomic approaches. In total, 1323 two-dimensional gel electrophoresis spots and 1652 identified proteins by isobaric tags for relative and absolute quantitation were quantitatively profiled during fiber elongation. Between allopolyploids and their diploid A- and D-genome progenitors, amounts of differential expression ranged from 4.4 to 12.8%. Over 80% of the allopolyploid proteome was additively expressed with respect to progenitor diploids. Interestingly, the fiber proteome of G. hirsutum resembles the parental A-genome more closely, where long, spinable fiber first evolved, than does the fiber proteome of G. barbadense. More protein expression patterns were A-dominant than D-dominant in G. hirsutum, but in G. barbadense, the direction of expression-level dominance switched from the D-genome to the A-genome during fiber development. Comparison of developmental changes between the two allopolyploid species revealed a high level of proteomic differentiation despite their shared ancestry, relatively recent evolutionary divergence, and similar gross morphology. These results suggest that the two allopolyploid species have achieved superficially similar modern fiber phenotypes through different evolutionary routes at the proteome level. We also detected homeolog-specific expression for 1001 proteins and present a novel approach to infer the relationship between homeolog-specific and duplicate expression patterns. Our study provides a proteomic perspective on understanding evolutionary consequences of allopolyploidization, showing how protein expression has been altered by polyploidization and subsequently has diversified among species.

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Gene expression dosage regulation in an allopolyploid fish.

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Gene expression dosage regulation in an allopolyploid fish.

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