title: An RNA-based approach to sequence the mitogenome of Hypoptopoma incognitum (Siluriformes: Loricariidae).
abstract: Hypoptopoma incognitum is a fish of the fifth most species-rich family of vertebrates and abundant in rivers from the Brazilian Amazon. Only two species of Loricariidae fish have their complete mitogenomes sequence deposited in the Genbank. An innovative RNA-based approach was used to assemble the complete mitogenome of H. incognitum with an average coverage depth of 5292×. The typical vertebrate mitochondrial features were found; 22 tRNA genes, two rRNA genes, 13 protein-coding genes, and a non-coding control region. Moreover, the use of this approach allowed the measurement of mtRNA expression levels, the punctuation pattern of editing, and the detection of heteroplasmies.
authors.affiliation: a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil .
authors.forename: Daniel Andrade
authors.initials: DA
authors.lastname: Moreira
authors.affiliation: a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil .
authors.forename: Maithê G P
authors.initials: MG
authors.lastname: Magalhães
authors.affiliation: a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil .
authors.forename: Paula C C
authors.initials: PC
authors.lastname: de Andrade
authors.affiliation: b Divisão de Genética , Instituto Nacional do Cancer (INCA) , Rio de Janeiro , Brasil , and.
authors.forename: Carolina
authors.initials: C
authors.lastname: Furtado
authors.affiliation: c Laboratório de Ecofisiologia e Evolução Molecular , Instituto Nacional de Pesquisas da Amazônia (INPA) , Manaus , Brasil.
authors.forename: Adalberto L
authors.initials: AL
authors.lastname: Val
authors.affiliation: a Laboratório de Toxicologia Ambiental , Fundação Oswaldo Cruz (FIOCRUZ) , Rio de Janeiro , Brasil .
authors.forename: Thiago Estevam
authors.initials: TE
authors.lastname: Parente
mesh_terms: D000818:Animals; D002397:Catfishes / Q000235:genetics*; D018388:Codon, Terminator; D004272:DNA, Mitochondrial / Q000235:genetics; D029941:Fish Proteins / Q000235:genetics; D023061:Gene Order; D020459:Genes, rRNA; D054629:Genome, Mitochondrial; D058977:Molecular Sequence Annotation; D012343:RNA, Transfer / Q000235:genetics; D017423:Sequence Analysis, RNA; D000073336:Whole Genome Sequencing
chemical_list: D018388:Codon, Terminator; D004272:DNA, Mitochondrial; D029941:Fish Proteins; D012343:RNA, Transfer
keywords: Fish; RNA-Seq; heteroplasmy; mtRNA; transcriptome