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Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree

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Abstract

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.

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Acknowledgements

The authors are grateful for the financial support from the Brazilian National Council for Scientific and Technological Development (CNPQ), Grant No. 479665/2011-7, and from The Brazilian Agricultural Research Corporation (EMBRAPA), Grant No. 01.11.07.002.00.00. J.M.P. received a graduate scholarship from FAPESP (Grant No. 2012/03553-8). We would like to thank EMBRAPA Multiuser Bioinformatics Lab (Laboratório Multiusuário de Bioinformática da Embrapa) for providing additional computational infrastructure; Daniel Chaves Webber for elaborating the map of cachara collection points (Fig. S1, Supplementary material); and Jefferson Cristiano Christofoletti for formatting the images in Figs. 4 and 5.

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Authors and Affiliations

  1. Embrapa Pesca e Aquicultura, CNPASA, Palmas, TO, Brazil

    Luciana Cristine Vasques Villela, Anderson Luis Alves & Eduardo Sousa Varela

  2. Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Veterinária, Universidade de Brasília (UnB), Brasília, DF, Brazil

    Luciana Cristine Vasques Villela & Alexandre Rodrigues Caetano

  3. Embrapa Informática Agropecuária, CNPTIA, Campinas, SP, Brazil

    Michel Eduardo Beleza Yamagishi & Poliana Fernanda Giachetto

  4. Embrapa Recursos Genéticos e Biotecnologia, CENARGEN, Brasília, DF, Brazil

    Naiara Milagres Augusto da Silva & Alexandre Rodrigues Caetano

  5. 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 Ponzetto

  6. Embrapa Labex EUA, Secretaria de Relações Internacionais, Brasília, DF, Brazil

    Samuel Rezende Paiva

  7. CNPq Fellow, Brasília, DF, Brazil

    Samuel Rezende Paiva & Alexandre Rodrigues Caetano

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  1. Luciana Cristine Vasques Villela
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  2. Anderson Luis Alves
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  3. Eduardo Sousa Varela
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Correspondence to Alexandre Rodrigues Caetano.

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Villela, L.C.V., Alves, A.L., Varela, E.S. et al. Complete mitochondrial genome from South American catfish Pseudoplatystoma reticulatum (Eigenmann & Eigenmann) and its impact in Siluriformes phylogenetic tree. Genetica 145, 51–66 (2017). https://doi.org/10.1007/s10709-016-9945-7

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