Genome-wide analysis of alternative splicing in Volvox carteri

Abstract

BackgroundAlternative splicing is an essential mechanism for increasing transcriptome and proteome diversity in eukaryotes. Particularly in multicellular eukaryotes, this mechanism is involved in the regulation of developmental and physiological processes like growth, differentiation and signal transduction.ResultsHere we report the genome-wide analysis of alternative splicing in the multicellular green alga Volvox carteri. The bioinformatic analysis of 132,038 expressed sequence tags (ESTs) identified 580 alternative splicing events in a total of 426 genes. The predominant type of alternative splicing in Volvox is intron retention (46.5%) followed by alternative 5′ (17.9%) and 3′ (21.9%) splice sites and exon skipping (9.5%). Our analysis shows that in Volvox at least ~2.9% of the intron-containing genes are subject to alternative splicing. Considering the total number of sequenced ESTs, the Volvox genome seems to provide more favorable conditions (e.g., regarding length and GC content of introns) for the occurrence of alternative splicing than the genome of its close unicellular relative Chlamydomonas. Moreover, many randomly chosen alternatively spliced genes of Volvox do not show alternative splicing in Chlamydomonas. Since the Volvox genome contains about the same number of protein-coding genes as the Chlamydomonas genome (~14,500 protein-coding genes), we assumed that alternative splicing may play a key role in generation of genomic diversity, which is required to evolve from a simple one-cell ancestor to a multicellular organism with differentiated cell types (Mol Biol Evol 31:1402-1413, 2014). To confirm the alternative splicing events identified by bioinformatic analysis, several genes with different types of alternatively splicing have been selected followed by experimental verification of the predicted splice variants by RT-PCR.ConclusionsThe results show that our approach for prediction of alternative splicing events in Volvox was accurate and reliable. Moreover, quantitative real-time RT-PCR appears to be useful in Volvox for analyses of relationships between the appearance of specific alternative splicing variants and different kinds of physiological, metabolic and developmental processes as well as responses to environmental changes.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-1117) contains supplementary material, which is available to authorized users.

Re‐annotation, improved large‐scale assembly and establishment of a catalogue of noncoding loci for the genome of the model brown alga Ectocarpus

“…It is difficult to precisely evaluate whether Ectocarpus exhibits a particularly low level of alternative splicing compared to other model organisms based on this value because estimates for these other organisms are constantly being revised as more extensive transcriptomic datasets become available. Based on current estimates, however, the frequency of alternative splicing in Ectocarpus falls within the range of 1.2–3.4 transcripts per intron‐containing gene proposed for diverse model organisms with intron‐rich genomes including humans, mouse, Drosophila melanogaster, Caenorhabditis elegans and Arabidopsis thaliana (Chen et al ., ; Kianianmomeni et al ., ; Lee & Rio, ; Zhang et al ., ), and therefore does not appear to be exceptionally low.…”

Alternative splicing and the evolution of phenotypic novelty

“…However, whether the proportion of conserved alternative splicing events per species covaries with the overall genome-wide prevalence of alternative splicing or with species complexity is unknown. In any case, increasing noise in alternative splicing regulation may, in itself, provide the substrate for selection by contributing to phenotypic variation creating a 'landscape of opportunities' [109,110].…”

Genome‐wide analysis of alternative splicing events in Hordeum vulgare: Highlighting retention of intron‐based splicing and its possible function through network analysis

“…The decisive factor in the choice of a sample gene was the potential modification of protein domains or protein sequence motifs by alternative splicing [82]. As a consequence of this approach, elongation factor family protein (MLOC_3412) selected.…”