Development of a universal double-digest RAD sequencing approach for a group of nonmodel, ecologically and economically important insect and fish taxa
| Autor: | Natalie B. Roberts, Kaitlin P. Coyle, Harry V. Daniels, M. O. Burford Reiskind, Reade B. Roberts, Michael H. Reiskind, Edward L. Vargo, Jennifer E. Schaff, Paul Labadie |
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| Rok vydání: | 2015 |
| Předmět: |
0301 basic medicine
Insecta Range (biology) media_common.quotation_subject ved/biology.organism_classification_rank.species Insect Biology Genome DNA sequencing 03 medical and health sciences Genetics Animals Model organism Ecology Evolution Behavior and Systematics media_common ved/biology Fishes DNA DNA Restriction Enzymes Genomics Sequence Analysis DNA Restriction enzyme 030104 developmental biology Taxon Evolutionary biology Fish Biotechnology |
| Zdroj: | Molecular ecology resources. 16(6) |
| ISSN: | 1755-0998 |
| Popis: | The generation of genome-scale data is critical for a wide range of questions in basic biology using model organisms, but also in questions of applied biology in nonmodel organisms (agriculture, natural resources, conservation and public health biology). Using a genome-scale approach on a diverse group of nonmodel organisms and with the goal of lowering costs of the method, we modified a multiplexed, high-throughput genomic scan technique utilizing two restriction enzymes. We analysed several pairs of restriction enzymes and completed double-digestion RAD sequencing libraries for nine different species and five genera of insects and fish. We found one particular enzyme pair produced consistently higher number of sequence-able fragments across all nine species. Building libraries off this enzyme pair, we found a range of usable SNPs between 4000 and 37 000 SNPS per species and we found a greater number of usable SNPs using reference genomes than de novo pipelines in STACKS. We also found fewer reads in the Read 2 fragments from the paired-end Illumina Hiseq run. Overall, the results of this study provide empirical evidence of the utility of this method for producing consistent data for diverse nonmodel species and suggest specific considerations for sequencing analysis strategies. |
| Databáze: | OpenAIRE |
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