Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids

Abstract

Polyploidy has been a common process during the evolution of eukaryotes, especially plants, leading to speciation and the evolution of new gene functions. Gene expression levels and patterns can change, and gene silencing can occur in allopolyploids-phenomena sometimes referred to as "transcriptome shock." Alternative splicing (AS) creates multiple mature mRNAs from a single type of precursor mRNA. Here we examined the evolution of AS patterns after polyploidy, with natural and two resynthesized allotetraploid Brassica napus lines, using RT-PCR and sequencing assays of 82 AS events in duplicated gene pairs (homeologs). Comparing the AS patterns between the two homeologs in natural B. napus revealed that many of the gene pairs show different AS patterns, with a few showing variation that was organ specific or induced by abiotic stress treatments. In the resynthesized allotetraploids, 26-30% of the duplicated genes showed changes in AS compared with the parents, including many cases of AS event loss after polyploidy. Parallel losses of many AS events after allopolyploidy were detected in the two independently resynthesized lines. More changes occurred in parallel between the two lines than changes specific to each line. The PASTICCINO gene showed partitioning of two AS events between the two homeologs in the resynthesized allopolyploids. AS changes after allopolyploidy were much more common than homeolog silencing. Our findings indicate that AS patterns can change rapidly after polyploidy, that many genes are affected, and that AS changes are an important component of the transcriptome shock experienced by new allopolyploids.gene duplication | whole genome duplication | molecular evolution P olyploidy is ubiquitous in plants, with many plants being evolutionarily recent polyploids, and all angiosperms having one or more ancient polyploidy events in their lineage (1-3). Polyploids can display novel phenotypes that may contribute to their evolutionary success (4). Gene expression levels and patterns in natural and synthetic polyploids have been widely studied to investigate the immediate and long-term effects of polyploidy. Some of the phenomena revealed include nonadditive patterns of gene expression in polyploids compared with their progenitors, divergence in expression levels and patterns between the homeologs, and gene silencing, with the effects being variable in different organ types, in different developmental stages, and in response to abiotic stresses (reviewed in refs. 5-8).Alternative splicing (AS) is a posttranscriptional mechanism that can regulate gene expression. AS also allows multiple proteins to be produced from the same gene. In addition, AS can cause transcript degradation by including premature stop codons within the coding region that target the transcripts for nonsensemediated decay, and potentially lower levels of gene expression (9, 10). Premature stop codons introduced by AS can sometimes result in truncated proteins that are functional (11). AS can result in phenotypic changes and impact m...

Whole-genome duplication in teleost fishes and its evolutionary consequences

“…Other studies exclusively identified divergent evolution in noncoding regions, while the coding sequence or gene function remained highly conserved. This was true for a duplicated gene pair of the argonaute (Ago) family, encoding AGO proteins important for small RNA mediated gene silencing (McFarlane et al, 2011), and for IGFBP-2 genes, binding and regulating actions of Insulinlike growth factor (Zhou et al, 2011). None of these studies reported identical expression patterns of TS-WGD duplicates, emphasizing that changes in regulatory elements are very common after WGD.…”

“…Divergence of splicing events can principally play a role after polyploidization as shown in a study in plants (Brassicaceae) (Zhou et al, 2011). In this study natural and resynthesized tetraploid species were compared to a closely related diploid species in terms of splicing patterns of paralogous genes.…”

Hybridization in Plants: Old Ideas, New Techniques

“…It has been demonstrated that, in some cases, allopolyploids can survive in a broader range of environments than their progenitors. This can be due to greater gene regulatory flexibility as a result of homologspecific gene regulation (Dong and Adams, 2011;Combes et al, 2012) or alternative splicing (Zhou et al, 2011) in response to environmental perturbation. However, there remains a need for more empirical evidence demonstrating ecological differentiation facilitated by allopolyploidy (Abbott et al, 2013;Madlung, 2013;Soltis et al, 2014).…”

Polyploidy and novelty: Gottlieb's legacy

“…The negative correlation between AS and duplication may relate to the 'expense' of operating the AS machinery: if the cost of generating multiple isoforms through AS is high, then selection would favour reducing it in those cases where multiple isoforms may be present through other mechanisms, such as gene duplication or polyploidy. Initial investigations of AS in relation to gene and genome duplication in plants have focused on Arabidopsis [70], Brassica napus [71] and wheat [72]. Additional studies of the role of AS in generating novel isoforms in polyploids are needed; for further information on AS in polyploids, see Yoo et al [23].…”