Comparative genomics and the evolution of amphibian chemical defense

• Main Author: Machado, Denis Jacob
• Publication Date: 2018
• Format: Doctoral thesis
• Language: eng
• Source: Biblioteca Digital de Teses e Dissertações da USP
• Download full: https://www.teses.usp.br/teses/disponiveis/95/95131/tde-20012023-095836/
• topic: Hyloxalus subpunctatus; Hyloxalus subpunctatus; Melanophryniscus moreirae; Melanophryniscus moreirae; Scaphiopus holbrookii; Scaphiopus holbrookii

Chapter 1 of this dissertation brings a discussion about the current state of basic and applied research on the evolution and biology of amphibians in general, and on amphibian chemical defense in particular. This introductory chapter also advocates comparative genomics as a strategy to increase our understanding of amphibian chemical defense and evolution, which is made possible thanks to high-throughput sequencing technologies but remains challenging mainly due to specific challenges of working with non-model organisms, including the lack of diverse and well-curated genomic databases. The remaining chapters are the first stepping-stones in the direction of a more extensive line of investigation that ultimately leads towards a multidisciplinary work that aims to enhance the transfer of knowledge between basic and applied research. Chapter 2 addresses the challenges in de novo assembly of mitogenomes of frogs when no reference sequence is available, and resources are limited. Chapter 3 introduces a new ad hoc mapping strategy to test the circularization of novel mitogenomes, using alignment scores and a new per-position sequence coverage value (which we named connectivity) to assess the quality of the inferred circularization. Chapter 4 address the assembly of the draft nuclear genomes of Scaphiopus holbrookii and Phyllobates terribilis, with focus on the homology-based and ab initio annotation of protein-coding genes and the proposal of new phylogenetic markers. Chapter 5 presents the de novo assembly of repetitive DNA in the nuclear genome of frogs, with new insights on the role of repeats in the variation of genome size in amphibians and new phylogenetic markers based on these genomic elements. Chapter 6 is a reply to Tarvin et al. (2016), including a review of the current knowledge about alkaloid defense in poison frogs. In combination, these chapters add to our infant but growing knowledge of amphibian genomics and chemical defense and strengthen the communication between basic research in non-model organisms and cutting-edge bioinformatic methods.