Novel genomic tool to study early stages of speciation in species with large genomes =...

Registro bibliográfico

  • Título: Novel genomic tool to study early stages of speciation in species with large genomes = Noveherramienta genómica para estudiar etapas tempranas de especiación en especies con grangenomas
  • Autor: Londoño Correa, Diego Alejandro
  • Publicación original: 2020
  • Descripción física: PDF
  • Nota general:
    • Colombia
  • Notas de reproducción original: Digitalización realizada por la Biblioteca Virtual del Banco de la República (Colombia)
  • Notas:
    • Resumen: Abstract: Thanks to theoretical and technological advances in evolutionary biology we can look into genomic patters to infer evolutionary processes such as divergence and gene flow, and how they shape the genomic landscape. However, such studies tend to focus on model species with small genomes and overlook non-model species with large repetitive genomes, thus missing generality across a big part of the tree of life. Here, we develop new genomic methods for the grasshopper Chorthippus parallelus, which is characterized by a giant genome of 13.5 Gb, which is not only expensive to sequence but impossible to assemble using state of the art methodologies. Alternative genomic methods involving Exome Capture have been developed in the last years to study other species with large repetitive genomes but these approaches have not been developed in grasshoppers yet. In this study we test two different library protocols — Nextera and Collibri — coupled with multiplexing, exome capture and Illumina sequencing. To test which library protocol was the best to be coupled with the exome capture we compared the number of retained reads and PCR duplicates in both protocols after sequencing. We found that Nextera was the library protocol with the highest number of retained reads and lowest number of PCR duplicates making it the best library protocol to be used in future studies. To test If the capture worked, these reads were mapped to a file containing target sequences and the coverage was then compared to the coverage resulting from a no-enrichment protocol. The capture protocol had a up to ~26 fold enrichment confirming that the baits hybridized with the target sequences. We also found that beads attached to the baits inhibit the polymerase, suggesting that beads should be removed before the amplification step. Two technical replicates showed consistent patterns but higher input of DNA seems to increase the efficiency of the capture. Together, our results suggest that this protocol could be used in organisms with large genomes, like grasshoppers, for which no reference genome is available, helping to fill the gaps in the knowledge of the genomic landscape of differentiation in these underrepresented species.
    • © Derechos reservados del autor
    • Colfuturo
  • Forma/género: tesis
  • Idioma: castellano
  • Institución origen: Biblioteca Virtual del Banco de la República
  • Encabezamiento de materia:

Web semántica