The divergence of alternative splicing between ohnologs in teleost fishes

Yuwei Wang,Baocheng Guo

doi:10.1186/s12862-021-01833-6

Abstract

BackgroundGene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations. The evolutionary link between gene duplication and AS is still controversial, due to utilizing duplicates from inconsistent ages of duplication events in earlier studies. With the aid of RNA-seq data, we explored evolutionary scenario of AS divergence between duplicates with ohnologs that resulted from the teleost genome duplication event in zebrafish, medaka, and stickleback.ResultsOhnologs in zebrafish have fewer AS forms compared to their singleton orthologs, supporting the function-sharing model of AS divergence between duplicates. Ohnologs in stickleback have more AS forms compared to their singleton orthologs, which supports the accelerated model of AS divergence between duplicates. The evolution of AS in ohnologs in medaka supports a combined scenario of the function-sharing and the accelerated model of AS divergence between duplicates. We also found a small number of ohnolog pairs in each of the three teleosts showed significantly asymmetric AS divergence. For example, the well-known ovary-factor gene cyp19a1a has no AS form but its ohnolog cyp19a1b has multiple AS forms in medaka, suggesting that functional divergence between duplicates might have result from AS divergence.ConclusionsWe found that a combined scenario of function-sharing and accelerated models for AS evolution in ohnologs in teleosts and rule out the independent model that assumes a lack of correlation between gene duplication and AS. Our study thus provided insights into the link between gene duplication and AS in general and ohnolog divergence in teleosts from AS perspective in particular.

Highlights

Gene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations
Transcript number difference between ohnologs in the three teleost fishes ;Ohnologs that resulted from teleost genome duplication (TGD) and singletons were retrieved from Inoue et al [33] (Additional file 1: Table S1)
We tackled the evolutionary link between gene duplication and AS using ohnologs that were generated by the TGD at same time in zebrafish, medaka, and stickleback

Summary

Introduction

Gene duplication and alternative splicing (AS) are two distinct mechanisms generating new materials for genetic innovations. With the aid of RNA-seq data, we explored evolutionary scenario of AS divergence between duplicates with ohnologs that resulted from the teleost genome duplication event in zebrafish, medaka, and stickleback. Gene duplication is a common phenomenon in genome, and is deeply believed to play important roles in organismal evolution [1]. Alternative splicing (AS), the production of different mature transcripts from the same primary RNA sequence, is a post-transcriptional process that allows a single gene to encode multiple proteins by including or. ~ 95% human multiple-exon genes show alternative splicing [20]. Multiple-exon genes tend to be retained long after duplication in various organisms [21, 22]. It would be interesting to know the divergence of AS between duplicates

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Discussion

Conclusion