De novo transcriptome assembly, annotation and comparison of four ecological and evolutionary model salmonid fish species ...
Abstract Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research...
| Main Authors: | , , , , , |
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| Format: | Article in Journal/Newspaper |
| Language: | unknown |
| Published: |
figshare
2018
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| Subjects: | |
| Online Access: | https://dx.doi.org/10.6084/m9.figshare.c.3971733 https://springernature.figshare.com/collections/De_novo_transcriptome_assembly_annotation_and_comparison_of_four_ecological_and_evolutionary_model_salmonid_fish_species/3971733 |
| Summary: | Abstract Background Salmonid fishes exhibit high levels of phenotypic and ecological variation and are thus ideal model systems for studying evolutionary processes of adaptive divergence and speciation. Furthermore, salmonids are of major interest in fisheries, aquaculture, and conservation research. Improving understanding of the genetic mechanisms underlying traits in these species would significantly progress research in these fields. Here we generate high quality de novo transcriptomes for four salmonid species: Atlantic salmon (Salmo salar), brown trout (Salmo trutta), Arctic charr (Salvelinus alpinus), and European whitefish (Coregonus lavaretus). All species except Atlantic salmon have no reference genome publicly available and few if any genomic studies to date. Results We used paired-end RNA-seq on Illumina to generate high coverage sequencing of multiple individuals, yielding between 180 and 210Â M reads per species. After initial assembly, strict filtering was used to remove duplicated, redundant, ... |
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