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Fouquet A, Ferrier B, Salmona J, Tirera S, Vacher JP, Courtois EA, Gaucher P, Lima JD, Nunes PMS, de Souza SM, Rodrigues MT, Noonan B, de Thoisy B. Phenotypic and life-history diversification in Amazonian frogs despite past introgressions. Mol Phylogenet Evol 2019; 130:169-180. [DOI: 10.1016/j.ympev.2018.09.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 09/15/2018] [Accepted: 09/15/2018] [Indexed: 10/28/2022]
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Jacob Machado D, Janies D, Brouwer C, Grant T. A new strategy to infer circularity applied to four new complete frog mitogenomes. Ecol Evol 2018; 8:4011-4018. [PMID: 29721275 PMCID: PMC5916287 DOI: 10.1002/ece3.3918] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Revised: 01/10/2018] [Accepted: 01/11/2018] [Indexed: 11/10/2022] Open
Abstract
We applied a novel strategy to infer sequence circularity and complete assembly of four mitochondrial genomes (mitogenomes) of the frog families Bufonidae (Melanophryniscus moreirae), Dendrobatidae (Hyloxalus subpunctatus and Phyllobates terribilis), and Scaphiopodidae (Scaphiopus holbrookii). These are the first complete mitogenomes of these four genera and Scaphiopodidae. We assembled mitogenomes from short genomic sequence reads using a baiting and iterative mapping strategy followed by a new ad hoc mapping strategy developed to test for assembly circularization. To assess the quality of the inferred circularization, we used Bowtie2 alignment scores and a new per-position sequence coverage value (which we named "connectivity"). Permutation tests with 400 iterations per specimen and 1% or 5% chance of mutation at the ends of the putative circular sequences showed that the proposed method is highly sensitive, with a single nucleotide insertion or deletion being sufficient for circularity to be rejected. False positives comprised only 2% of all observations and possessed significantly lower alignment scores. The size, gene content, and gene arrangement of each mitogenome differed among the species but matched the expectations for their clades. We argue that basic studies on circular sequences can benefit from the results and bioinformatics procedures introduced here, especially when closely related references are lacking.
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Affiliation(s)
- Denis Jacob Machado
- Bioinformatics Interunits Graduate ProgramUniversity of São PauloSão PauloBrazil
| | - Daniel Janies
- Department of Bioinformatics and GenomicsUNC CharlotteCharlotteNCUSA
| | - Cory Brouwer
- Department of Bioinformatics and GenomicsUNC CharlotteCharlotteNCUSA
- UNC Charlotte Bioinformatics Service DivisionKannapolisNCUSA
| | - Taran Grant
- Department of ZoologyUniversity of São PauloSão PauloBrazil
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Grant T, Rada M, Anganoy-Criollo M, Batista A, Dias PH, Jeckel AM, Machado DJ, Rueda-Almonacid JV. Phylogenetic Systematics of Dart-Poison Frogs and Their Relatives Revisited (Anura: Dendrobatoidea). SOUTH AMERICAN JOURNAL OF HERPETOLOGY 2017. [DOI: 10.2994/sajh-d-17-00017.1] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Affiliation(s)
- Taran Grant
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
- Amphibian Collection, Museum of Zoology of the University of São Paulo, 04263-000, São Paulo, SP, Brazil
| | - Marco Rada
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Marvin Anganoy-Criollo
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Abel Batista
- Universidad Autónoma de Chiriquí, David, Republic of Panama
- Los Naturalistas, David 0426-01459, Chiriquí, Panama
| | - Pedro Henrique Dias
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Adriana Moriguchi Jeckel
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
| | - Denis Jacob Machado
- Department of Zoology, Institute of Biosciences, University of São Paulo, 05508-090, São Paulo, SP, Brazil
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