| Autor: |
André Gomes-dos-Santos, Elsa Froufe, John Pfeiffer, Chase Smith, Andre Machado, L Filipe C Castro, Van Do, Akimasa Hattori, Nicole Garrison, Nathan Whelan, Ivan Bolotov, Ilya Vikhrev, Alexander Kondakov, Mohamed Ghamizi, Vincent Prié, Arthur Bogan, Manuel Lopes-Lima |
| Rok vydání: |
2022 |
| DOI: |
10.22541/au.166799900.04572038/v2 |
| Popis: |
The proliferation of genomic sequencing approaches has significantly impacted the field of phylogenetics. Target capture approaches provide a cost-effective, fast, and easily applied strategy for phylogenetic inference of non-model organisms. However, many existing pipelines used to create phylogenomic datasets from target capture data are incapable of incorporating whole genome sequencing data into their workflows. Here, we develop a highly efficient pipeline for capturing and de novo assembly of the targeted regions using whole genome re-sequencing reads. This new pipeline allows capturing targeted loci accurately and efficiently, and given its unbiased nature, can easily be expanded to be used with any other target capture probe set. We demonstrate the utility of our approach by incorporating whole genome sequencing data into a recently developed target capture probe set to reconstruct the evolutionary history of the freshwater mussel family Margaritiferidae, reconstructing supraspecific relationships outside the Unionidae family, providing the first comprehensive multi-loci phylogeny of the Margaritiferidae. We also provide a catalogue of well-curated functional annotations of the targeted regions for the target capture probe set, representing a complementary tool for scrutinizing phylogenetic inferences while expanding future applications of the probe set. |
| Databáze: |
OpenAIRE |
| Externí odkaz: |
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