Whole-genome sequence of the eastern spadefoot toad, Scaphiopus holbrookii (Amphibia: Anura: Scaphiopodidade) and of the Maldonado redbelly toad, Melanophryniscus moreirae (Amphibia: Anura: Bufonidae)

• Grant number: 15/18654-2
• Support Opportunities: Scholarships abroad - Research Internship - Doctorate
• Start date: January 29, 2016
• End date: January 28, 2017
• Field of knowledge: Interdisciplinary Subjects
• Principal Investigator: Taran Grant
• Grantee: Denis Jacob Machado
• Supervisor: Daniel Andrew Janies
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Institution abroad: University of North Carolina at Charlotte (UNCC), United States
• Associated to the scholarship: 13/05958-8 - Comparative Genomics and the Evolution of Amphibian Chemical Defense, BP.DR

Abstract

Despite the availability of second-generation sequencing technologies that allows rapid acquisition of molecular data at feasible prices, computational difficulties in analyzing large sequence datasets and the lack of reference genomes for frogs have posed difficulties to the advance of anuran genomics. To date, only two whole-genomes and 81 complete mitochondrial genomes have been published for Anura, a very small representation of the current 6482 species of frogs. Here I propose to assemble and analyze the partial nuclear and complete mitochondrial genome of the Eastern spadefoot toad, Scaphiopus holbrookii (Scaphiopodidae), and of the Maldonado redbelly toad, Melanophryniscus moreirae (Bufonidae), using second-generation sequencing technology (Illumina HiSeq). These species have been selected due to their tractable genetics in relation to other species of Anura and Bufonidae, respectively. Also, both species can allow us to address specific questions regarding amphibian evolution and their chemical defensive mechanisms. The Eastern spadefoot have strategic phylogenetic positions, which might allow us to ask questions about genome evolution at the aquatic to terrestrial transition in frogs, the role of transposable elements in amphibian genome sizes, lineage- and anuran-specific highly-conserved elements, the evolution of organelle genes and mitochondrial genome arrangements in Anura, among others. The Maldonado redbelly toad is a bufonid in which large quantities of dietary alkaloids and the biosynthesized indolealkylamine bufotenine co-occur, which makes it strategic to our understanding of anuran chemical defense. The viability of this project will be guaranteed by the availability of raw sequences, massive computational resources and the expert collaboration that I will receive at the foreign institution. I hope this project will take us one step further in overcoming both our current lack of knowledge in anuran genomics and the gap between the easy gathering of second-generation sequencing data and the computational difficulties in analyzing it. (AU)

Scientific publications

(5)

(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, DENIS JACOB; CASTROVIEJO-FISHER, SANTIAGO; GRANT, TARAN. Evidence of absence treated as absence of evidence: The effects of variation in the number and distribution of gaps treated as missing data on the results of standard maximum likelihood analysis. Molecular Phylogenetics and Evolution, v. 154, JAN 2021. (12/10000-5, 15/18654-2, 18/15425-0)

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)