Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish:Proof of concept for key components of the insulin-like growth factor axis
| Autor: | Fiona M Lappin, Daniel J. Macqueen, Rebecca L Shaw |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2016 |
| Předmět: |
0301 basic medicine
Fish Proteins Genome evolution Salmonidae/genetics Genomics Sequence Analysis DNA/veterinary Biology Aquatic Science Genome Evolution Molecular 03 medical and health sciences Phylogenetics Somatomedins Somatomedins/genetics Gene Duplication Genetics Animals Fish Proteins/genetics High-Throughput Nucleotide Sequencing/veterinary Gene Illumina dye sequencing Phylogeny Phylogenetic tree High-Throughput Nucleotide Sequencing Sequence Analysis DNA 030104 developmental biology Evolutionary biology Genome Biology Genome/genetics Salmonidae |
| Zdroj: | Lappin, F M, Shaw, R L & Macqueen, D J 2016, ' Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish : Proof of concept for key components of the insulin-like growth factor axis ', Marine Genomics, vol. 30, pp. 15-26 . https://doi.org/10.1016/j.margen.2016.06.003 |
| DOI: | 10.1016/j.margen.2016.06.003 |
| Popis: | High-throughput sequencing has revolutionised comparative and evolutionary genome biology. It has now become relatively commonplace to generate multiple genomes and/or transcriptomes to characterize the evolution of large taxonomic groups of interest. Nevertheless, such efforts may be unsuited to some research questions or remain beyond the scope of some research groups. Here we show that targeted high-throughput sequencing offers a viable alternative to study genome evolution across a vertebrate family of great scientific interest. Specifically, we exploited sequence capture and Illumina sequencing to characterize the evolution of key components from the insulin-like growth (IGF) signalling axis of salmonid fish at unprecedented phylogenetic resolution. The IGF axis represents a central governor of vertebrate growth and its core components were expanded by whole genome duplication in the salmonid ancestor ~95Ma. Using RNA baits synthesised to genes encoding the complete family of IGF binding proteins (IGFBP) and an IGF hormone (IGF2), we captured, sequenced and assembled orthologous and paralogous exons from species representing all ten salmonid genera. This approach generated 299 novel sequences, most as complete or near-complete protein-coding sequences. Phylogenetic analyses confirmed congruent evolutionary histories for all nineteen recognized salmonid IGFBP family members and identified novel salmonid-specific IGF2 paralogues. Moreover, we reconstructed the evolution of duplicated IGF axis paralogues across a replete salmonid phylogeny, revealing complex historic selection regimes - both ancestral to salmonids and lineage-restricted - that frequently involved asymmetric paralogue divergence under positive and/or relaxed purifying selection. Our findings add to an emerging literature highlighting diverse applications for targeted sequencing in comparative-evolutionary genomics. We also set out a viable approach to obtain large sets of nuclear genes for any member of the salmonid family, which should enable insights into the evolutionary role of whole genome duplication before additional nuclear genome sequences become available. |
| Databáze: | OpenAIRE |
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