Alternative splicing in teleost fish genomes: same-species and cross-species analysis and comparisons.
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.
Lu
Jianguo
J
The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL 36849, USA.
Peatman
Eric
E
Wang
Wenqi
W
Yang
Qing
Q
Abernathy
Jason
J
Wang
Shaolin
S
Kucuktas
Huseyin
H
Liu
Zhanjiang
Z
D017398:Alternative Splicing / Q000235:genetics*; D000818:Animals; D002874:Chromosome Mapping; D016000:Cluster Analysis; D030541:Databases, Genetic; D020224:Expressed Sequence Tags; D005399:Fishes / Q000235:genetics*; D049810:Genetic Speciation; D016678:Genome / Q000502:physiology; D008954:Models, Biological; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
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