Global Analysis of the Small RNA Transcriptome in Different Ploidies and Genomic Combinations of a Vertebrate Complex – The Squalius alburnoides

Angela Inácio,Luca Comai,Patrícia Matos Pereira,Joana Pinho,Maria Manuela Coelho

doi:10.1371/journal.pone.0041158

Angela Inácio, Luca Comai + Show 3 more

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https://doi.org/10.1371/journal.pone.0041158

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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 showed that in response to the increase in genome dosage, triploids 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 in order to explore the miRNA involvement in gene expression regulation of triploids. Using high-throughput arrays and sequencing technologies we were able to verify that diploid and triploid hybrids shared most of their sequences and their miRNA expression profiles were high correlated. However, an overall view indicates an up-regulation of several miRNAs in triploids and a global miRNA expression in triploids higher than the predicted from an additive model. Those results point to a participation of miRNAs in the cellular functional stability needed when the ploidy change.

Highlights

The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates
In the southern basins, the fish is sympatric with the parental species S. pyrenaicus (P genome), which still interacts with the complex as a sperm donor and acts as source of genetic material [1]
Our aim is to explore miRNA involvement in gene expression regulation needed to control the potential genomic shock created by frequent events of hybridization and polyploidization in the S. alburnoides complex

Summary

Introduction

The Squalius alburnoides complex (Steindachner) is one of the most intricate hybrid polyploid systems known in vertebrates. This cyprinid fish forms a widely distributed complex endemic to the Iberian Peninsula. It originated by hybridization between a female Squalius pyrenaicus (Gunther) (P genome) and an already extinct paternal ancestor related to Anaecypris hispanica (Steindachner) (A genome) [1]. A characteristic feature of the S. alburnoides complex is its high reproductive diversity. This promotes intricately networked genetic exchanges and continuous shifting between different genetic forms. AA is extinct as an independent species but is frequently reconstituted from the complex (Figure 1)

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