Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree.
The cachara (Pseudoplatystoma reticulatum) is a Neotropical freshwater catfish from family Pimelodidae (Siluriformes) native to Brazil. The species is of relative economic importance for local aquaculture production and basic biological information is under development to help boost efforts to domesticate and raise the species in commercial systems. The complete cachara mitochondrial genome was obtained by assembling Illumina RNA-seq data from pooled samples. The full mitogenome was found to be 16,576 bp in length, showing the same basic structure, order, and genetic organization observed in other Pimelodidae, with 13 protein-coding genes, 2 rNA genes, 22 trNAs, and a control region. Observed base composition was 24.63% T, 28.47% C, 31.45% A, and 15.44% G. With the exception of NAD6 and eight tRNAs, all of the observed mitochondrial genes were found to be coded on the H strand. A total of 107 SNPs were identified in P. reticulatum mtDNA, 67 of which were located in coding regions. Of these SNPs, 10 result in amino acid changes. Analysis of the obtained sequence with 94 publicly available full Siluriformes mitogenomes resulted in a phylogenetic tree that generally agreed with available phylogenetic proposals for the order. The first report of the complete Pseudoplatystoma reticulatum mitochondrial genome sequence revealed general gene organization, structure, content, and order similar to most vertebrates. Specific sequence and content features were observed and may have functional attributes which are now available for further investigation.
Embrapa Pesca e Aquicultura, CNPASA, Palmas, TO, Brazil.|Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Veterinária, Universidade de Brasília (UnB), Brasília, DF, Brazil.
Luciana Cristine Vasques
LC
Villela
Embrapa Pesca e Aquicultura, CNPASA, Palmas, TO, Brazil.
Anderson Luis
AL
Alves
Embrapa Pesca e Aquicultura, CNPASA, Palmas, TO, Brazil.
Eduardo Sousa
ES
Varela
Embrapa Informática Agropecuária, CNPTIA, Campinas, SP, Brazil.
Michel Eduardo Beleza
ME
Yamagishi
Embrapa Informática Agropecuária, CNPTIA, Campinas, SP, Brazil.
Poliana Fernanda
PF
Giachetto
Embrapa Recursos Genéticos e Biotecnologia, CENARGEN, Brasília, DF, Brazil.
Naiara Milagres Augusto
NM
da Silva
Programa de Pós-Graduação em Genética Evolutiva e Biologia Molecular, Centro de Ciências Biológicas e da Saúde, Universidade Federal de São Carlos (UFSCar), São Carlos, SP, Brazil.
Josi Margarete
JM
Ponzetto
Embrapa Labex EUA, Secretaria de Relações Internacionais, Brasília, DF, Brazil.|CNPq Fellow, Brasília, DF, Brazil.
Samuel Rezende
SR
Paiva
Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Veterinária, Universidade de Brasília (UnB), Brasília, DF, Brazil. alexandre.caetano@embrapa.br.|Embrapa Recursos Genéticos e Biotecnologia, CENARGEN, Brasília, DF, Brazil. alexandre.caetano@embrapa.br.|CNPq Fellow, Brasília, DF, Brazil. alexandre.caetano@embrapa.br.
Alexandre Rodrigues
AR
Caetano
D000818:Animals; D001482:Base Composition; D001483:Base Sequence; D002397:Catfishes / Q000145:classification* / Q000235:genetics*; D003062:Codon; D019295:Computational Biology / Q000379:methods; D050259:Genes, Mitochondrial; D054629:Genome, Mitochondrial; D059014:High-Throughput Nucleotide Sequencing; D058977:Molecular Sequence Annotation; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide
D003062:Codon
Catfish; Mitogenome; Phylogenetic analysis; RNA-Seq; SNPs; Siluriformes