Gene expression dosage regulation in an allopolyploid fish

PloS One
Isa MatosM M Coelho

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 tr...Continue Reading

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Citations

Mar 8, 2019·Scientific Reports·Isa MatosMaria Manuela Coelho
May 28, 2020·Scientific Reports·Victor SpangenbergOxana Kolomiets

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Datasets Mentioned

BETA
E-MTAB-3174

Methods Mentioned

BETA
RNA-seq
PCR
PCRs
genotyping

Software Mentioned

Stampy
HTSeq
DAVID
liv
PP
TGICL
ArrayExpress
Bioconductor EDASeq
ESTScan
Ensembl

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