A new strategy to infer circularity applied to four new complete frog mitogenomes

Autor(es)

Machado, Denis Jacob ^[1] ; Janies, Daniel ^[2] ; Brouwer, Cory ^{[2, 3]} ; Grant, Taran ^[4]

Afiliação do(s) autor(es)

^[1] Univ Sao Paulo, Bioinformat Interunits Grad Program, Sao Paulo - Brazil

^[2] UNC Charlotte, Dept Bioinformat & Genom, Charlotte, NC - USA

^[3] UNC Charlotte Bioinformat Serv Div, Kannapolis, NC - USA

^[4] Univ Sao Paulo, Dept Zool, Sao Paulo - Brazil

• Tipo de documento: Artigo Científico
• Fonte: ECOLOGY AND EVOLUTION; v. 8, n. 8, p. 4011-4018, APR 2018.
• Citações Web of Science: 3

Resumo

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. (AU)

• Processo FAPESP: 12/10000-5 - Uma abordagem multidisciplinar para o estudo da diversificação de anfíbios
• Beneficiário: Taran Grant
• Modalidade de apoio: Auxílio à Pesquisa - Jovens Pesquisadores
• Processo FAPESP: 15/18654-2 - Sequenciamento genômico do sapo pé-de-pá-oriental, Scaphiopus holbrookii (Amphibia: Anura: Scaphiopodidade) e do sapo flamenguinho, Melanophryniscus moreirae (Amphibia: Anura: Bufonidae)
• Beneficiário: Denis Jacob Machado
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Doutorado
• Processo FAPESP: 13/05958-8 - Genômica Comparada e a Evolução da Defesa Química em Anfíbios
• Beneficiário: Denis Jacob Machado
• Modalidade de apoio: Bolsas no Brasil - Doutorado