Evolution of alternative splice variation and exon usage following whole genome duplication

• Main Author: Sandholm, Ronja Marlonsdotter
• Other Authors: Sandve, Simen Rød, Kent, Matthew Peter, Strand, Marius André
• Format: Master Thesis
• Language: English
• Published: Norwegian University of Life Sciences, Ås 2022
• Subjects: Atlantic salmon
• Online Access: https://hdl.handle.net/11250/3026606

Whole genome duplication and alternative splicing are two mechanisms that contribute to protein diversity. Whole genome duplication doubles the genetic material in an organism, providing raw material for adaptation and evolution of novel traits. Alternative splicing contributes to the proteome complexity, as it gives a gene the ability to produce several mRNA isoforms by alternatively splicing gene transcripts. While both processes are important factors in increasing protein diversity, their relationship is not well understood. The two primary aims of this thesis were to use Oxford Nanopore long-read RNA sequencing to better characterize the isoform diversity in Atlantic salmon and look for patterns of alternative splicing evolution following the salmonid-specific whole genome duplication event. With the long-read RNA sequences, we found that the majority (75%) of isoforms that mapped to known genes in the Atlantic salmon reference genome were previously unannotated; however, the annotated isoforms were more highly expressed. The diversity of isoforms was then used to test the models of alternative splicing evolution following whole genome duplication: the independent model, the function-sharing model, and the accelerated alternative splicing model. Our results did not support either the accelerated alternative splicing or function-sharing model, indicating no strong relationship between alternative splicing evolution and genes duplicated in the salmonid-specific whole genome duplication event. Helgenomeduplikasjon og alternativ spleising er to mekanismer som øker proteindiversitet. WGD fordobler en organismes genetiske materiale, noe som gir råmaterial for evolusjon av nye egenskaper, og for tilpasningsdyktighet. Alternativ spleising bidrar til å øke proteindiversiteten ettersom et gen kan produsere flere mRNA-isoformer ved å alternativt spleise transkripter. Selv om begge prosessene er viktige bidrag til økt proteindiversitet, er forholdet mellom dem ikke godt forstått. De to hovedmålene med denne ...