Denis Jacob Machado, Daniel James, Cory Brouwer, and Taran Grant (2018). A new strategy to infer circularity applied to four new complete frog mitogenomes. Ecology and Evolution, 8, 4011-4018.
Bioinformatics Interunits Graduate Program, University of São Paulo, São Paulo, Brazil
Department of Bioinformatics and Genomics, UNC Charlotte, Charlotte, NC, USA
UNC Charlotte Bioinformatics Service Division, Kannapolis, NC, USA
Department of Zoology, University of São Paulo, São Paulo, Brazil
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.