Comparative Genomics and the Evolution of Amphibian Chemical Defense

• Grant number: 13/05958-8
• Support Opportunities: Scholarships in Brazil - Doctorate
• Start date: June 01, 2013
• End date: February 28, 2018
• Field of knowledge: Biological Sciences - Zoology
• Principal Investigator: Taran Grant
• Grantee: Denis Jacob Machado
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 15/18654-2 - Whole-genome sequence of the eastern spadefoot toad, Scaphiopus holbrookii (Amphibia: Anura: Scaphiopodidade) and of the Maldonado redbelly toad, Melanophryniscus moreirae (Amphibia: Anura: Bufonidae), BE.EP.DR

Abstract

Here we propose to integrate next-generation sequencing (NGS) technologies into studies of the evolution of chemical defense in poison frogs. From a phylogenetic standpoint, the integration of NGS technologies into phylogenetic systematics promises to lead to more severely tested and complete hypotheses and provide new options for studying the evolution of chemical defense in amphibians. From a genomics perspective, comparative analysis of poison frogs and other anurans has great potential to identify the genetic changes that underly the molecular basis of amphibian chemical defense (i.e., lipophilic alkaloid sequestration and physiological resistance), which will point to new directions for future research. In this context, we will employ NGS (Illumina® HiSeqTM 2000) to generate six complete nuclear genomes from anuran amphibians with focus on poison frogs. These data will be employed to (1) search for specific genomic features potentially implicated in alkaloid sequestration and/or resistance in poison frogs and (2) design probe sets for target enrichment to allow us to use NGS methods to generate data for phylogenetic analysis of amphibians at different levels of divergence.

Scientific publications

(6)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

GRANT, TARAN; RADA, MARCO; ANGANOY-CRIOLLO, MARVIN; BATISTA, ABEL; DIAS, PEDRO HENRIQUE; JECKEL, ADRIANA MORIGUCHI; MACHADO, DENIS JACOB; RUEDA-ALMONACID, JOSE VICENTE. Phylogenetic Systematics of Dart-Poison Frogs and their Relatives Revisited (Anura: Dendrobatoidea). South American Journal of Herpetology, v. 12, n. 1, p. S1-S90, SEP 2017. (12/10000-5, 13/20420-4, 08/50928-1, 16/09999-9, 15/11239-0, 13/05958-8, 15/18654-2)

MACHADO, DENIS JACOB; DE LUNA MARQUES, FERNANDO PORTELLA; JIMENEZ-FERBANS, LARRY; GRANT, TARAN. An empirical test of the relationship between the bootstrap and likelihood ratio support in maximum likelihood phylogenetic analysis. CLADISTICS, DEC 2021. (18/15425-0, 15/18654-2, 13/05958-8, 12/10000-5)

GRANT, TARAN; RADA, MARCO; ANGANOY-CRIOLLO, MARVIN; BATISTA, ABEL; DIAS, PEDRO HENRIQUE; JECKEL, ADRIANA MORIGUCHI; MACHADO, DENIS JACOB; RUEDA-ALMONACID, JOSE VICENTE. Phylogenetic Systematics of Dart-Poison Frogs and their Relatives Revisited (Anura: Dendrobatoidea). South American Journal of Herpetology, v. 12, p. 90-pg., 2017-09-01. (15/18654-2, 13/20420-4, 13/05958-8, 08/50928-1, 16/09999-9, 15/11239-0, 12/10000-5)

MACHADO, D. J.; LYRA, M. L.; GRANT, T.. Mitogenome assembly from genomic multiplex libraries: comparison of strategies and novel mitogenomes for five species of frogs. MOLECULAR ECOLOGY RESOURCES, v. 16, n. 3, p. 686-693, MAY 2016. (12/10000-5, 13/05958-8)

MACHADO, DENIS JACOB; JANIES, DANIEL; BROUWER, CORY; GRANT, TARAN. A new strategy to infer circularity applied to four new complete frog mitogenomes. ECOLOGY AND EVOLUTION, v. 8, n. 8, p. 4011-4018, APR 2018. (12/10000-5, 15/18654-2, 13/05958-8)

MACHADO, DENIS JACOB. YBYRA facilitates comparison of large phylogenetic trees. BMC Bioinformatics, v. 16, JUL 1 2015. (12/10000-5, 13/05958-8, 09/13561-5)

Academic Publications

(References retrieved automatically from State of São Paulo Research Institutions)

MACHADO, Denis Jacob. Comparative genomics and the evolution of amphibian chemical defense. 2018. Doctoral Thesis - Universidade de São Paulo (USP). Instituto de Matemática e Estatística (IME/SBI) São Paulo.