Molecular Genetics and Genomics

, Volume 283, Issue 6, pp 531–539 | Cite as

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

  • Jianguo Lu
  • Eric Peatman
  • Wenqi Wang
  • Qing Yang
  • Jason Abernathy
  • Shaolin Wang
  • Huseyin Kucuktas
  • Zhanjiang LiuEmail author
Original Paper


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 (~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.


Alternative splicing Teleost Fish Genome Duplication 



We would like to thank Dr. Bing-bing Wang for sharing the ASviewer software with us. This research was supported in part by funding from the USDA’s National Institute of Food and Agriculture.

Supplementary material

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Copyright information

© Springer-Verlag 2010

Authors and Affiliations

  • Jianguo Lu
    • 1
  • Eric Peatman
    • 1
  • Wenqi Wang
    • 1
    • 2
  • Qing Yang
    • 3
  • Jason Abernathy
    • 1
  • Shaolin Wang
    • 1
  • Huseyin Kucuktas
    • 1
  • Zhanjiang Liu
    • 1
    Email author
  1. 1.The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, Department of Fisheries and Allied Aquacultures and Program of Cell and Molecular BiosciencesAuburn UniversityAuburnUSA
  2. 2.College of Animal SciencesQingdao Agricultural UniversityQingdaoChina
  3. 3.Department of Computer Science and Software EngineeringAuburn UniversityAuburnUSA

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