Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons

Abstract

Alternative splicing (AS) is a mechanism by which the coding diversity of the genome can be greatly increased. Rates of AS are known to vary according to the complexity of eukaryotic species potentially explaining the tremendous phenotypic diversity among species with similar numbers of coding genes. Little is known, however, about the nature or rate of AS in teleost fish. Here, we report the characteristics of AS in teleost fish and classification and frequency of five canonical AS types. We conducted both same-species and cross-species analysis utilizing the Genome Mapping and Alignment Program (GMAP) and an AS pipeline (ASpipe) to study AS in four genome-enabled species (Danio rerio, Oryzias latipes, Gasterosteus aculeatus, and Takifugu rubripes) and one species lacking a complete genome sequence, Ictalurus punctatus. AS frequency was lowest in the highly duplicated genome of zebrafish (17% of mapped genes). The compact genome of the pufferfish showed the highest occurrence of AS (approximately 43% of mapped genes). An inverse correlation between AS frequency and genome size was consistent across all analyzed species. Cross-species comparisons utilizing zebrafish as the reference genome allowed the identification of additional putative AS genes not revealed by zebrafish transcripts. Approximately, 50% of AS genes identified by same-species comparisons were shared among two or more species. A searchable website, the Teleost Alternative Splicing Database, was created to allow easy identification and visualization of AS transcripts in the studied teleost genomes. Our results and associated database should further our understanding of alternative splicing as an important functional and evolutionary mechanism in the genomes of teleost fish.

Molecular characterization and comparative expression analysis of two teleostean pro-inflammatory cytokines, IL-1β and IL-8, from Sebastes schlegeli

“…In the coding region, the lengths of exons are highly similar to vertebrates suggesting the functional conservation of the IL-8 gene as an essential chemokine in the animal kingdom. Even though IL-8 genomic sequence is highly similar among vertebrate species, it is possible to have splice variants due to differences in mRNA processing (Lu et al, 2010) and RNA editing (Li et al, 1999). Extensive studies on the genomic DNA of rainbow trout have identified novel isotypes of rainbow trout IL-8 (Fujiki et al, 2003).…”

Evidence for widespread subfunctionalization of splice forms in vertebrate genomes

“…This difference is likely the consequence of the relative contribution of gene duplication and alternative splicing to genome expansion in each lineage. Zebrafish have very high rates of gene duplication (Lu et al 2012) and display very low levels of alternative splicing (Lu et al 2010), while the inverse is true for humans (Shoja and Zhang 2006;Keren et al 2010). Therefore, it is not surprising that the effects of subfunctionalization will be amplified in a genomic background replete with alternative splicing yet relatively free of duplicate genes, as is the case with the human genome.…”

Diversity of teleost leukocyte molecules: Role of alternative splicing

“…Alternative splicing in teleost fish genomes has recently been analyzed in four species of fish, including zebrafish (Danio rerio), medaka (Oryzias latipes), stickleback (Gasterosteus aculeatus) and fugu (Takifugu rubripes) [13]. Interestingly, the frequency of AS was lowest in the highly duplicated genome of zebrafish (17% of mapped genes) and highest in the most compact genome of the pufferfish (43% of mapped genes) [13].…”

“…Interestingly, the frequency of AS was lowest in the highly duplicated genome of zebrafish (17% of mapped genes) and highest in the most compact genome of the pufferfish (43% of mapped genes) [13]. Several immune related-genes, such as interleukins, cytokine receptors, chemokines, TLR and some cell surface molecular markers, undergo AS, indicating that the immune function may also be regulated by AS in teleost fish.…”