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Genetics and Molecular Biology

Print version ISSN 1415-4757On-line version ISSN 1678-4685

Genet. Mol. Biol. vol.39 no.4 Ribeirão Preto Oct./Dec. 2016  Epub Sep 19, 2016

https://doi.org/10.1590/1678-4685-gmb-2016-0007 

Genomics and Bioinformatics

The complete mitochondrial genome of the threatened Neotropical catfish Lophiosilurus alexandri (Silurifomes: Pseudopimelodidae) and phylogenomic analysis indicate monophyly of Pimelodoidea

Daniel Cardoso Carvalho1 

Violeta da Rocha Perini2 

Alex Schomaker Bastos2  *

Igor Rodrigues da Costa2 

Ronald Kennedy Luz3 

Carolina Furtado4 

Francisco Prosdocimi2 

1Laboratório de Genética da Conservação, Programa de Pós-Graduação em Biologia dos Vertebrados, Pontifícia Universidade Católica de Minas Gerais (PUC Minas), Belo Horizonte, MG, Brazil.

2Laboratório de Genômica e Biodiversidade, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.

3Laboratório de Aquacultura da Escola de Veterinária da Universidade Federal de Minas Gerais (UFMG, Belo Horizonte, MG, Brazil.

4Instituto Nacional do Câncer (INCA), Rio de Janeiro, RJ, Brazil.


Abstract

Lophiosilurus alexandri is an endemic catfish from the São Francisco River Basin (Brazil) popularly known as pacamã, which has economic potential for aquaculture farming. The mitochondrial genome was sequenced for the threatened Neotropical catfish L. alexandri. Assembly into scaffolds using MIRA and MITObim software produced the whole, circularized mitochondrial genome, which comprises 16,445 bp and presents the typical gene arrangement of Teleostei mitochondria. A phylogenomic analysis was performed after the concatenation of all proteins obtained from whole mitogenomes of 20 Siluriformes and two outgroups. The results confirmed the monophyly of nine families of catfishes and also clustered L. alexandri as a sister group to the family Pimelodidae, thus confirming the monophyly of the superfamily Pimelodoidea. This is the first mitochondrial phylogenomics study for Pimelodoidea and the first mitogenome described for the Pseudopimelodidae family, representing an important resource for phylogeography, evolutionary biology, and conservation genetics studies in Neotropical fishes.

Keywords Mitogenome; fish; next-generation-sequencing; Illumina; Pseudopimelodidae

Catfishes (Siluriformes) are a highly diverse order composed of 39 families and more than 3,700 living species (Eschmeyer and Fong, 2016). The fish Lophiosilurus alexandri (Steindachner, 1877), popularly known as pacamã, is an endemic catfish from the São Francisco River Basin (Brazil) and belongs to the Pseudopimelodidae family, a taxon broadly distributed in South America (Eschmeyer and Fong, 2016). L. alexandri is a carnivorous species that displays parental care and has economic potential for aquaculture farming (Sato et al., 2003; dos Santos and Luz, 2009).

Pacamã may be cultivated in captivity after adapting broodstock to aquaculture conditions (Costa et al., 2015), however its natural populations have declined over the last decades. Threats such as overfishing and environmental degradation led to the inclusion of L. alexandri in the Brazilian red list of threatened species (Brasil, 2014).

Here we present the complete, circularized version of the whole mitochondrial genome and the phylogenomic relationships of pacamã to 20 other related Siluriformes and two outgroups using a supermatrix approach.

Muscle fragments were obtained from a freshly captured L. alexandri. The voucher specimen was fixed in 10% formalin and later preserved in 70% ethanol. (voucher: LGC6088 at PUC Minas Natural History Museum). Genomic DNA was extracted using a modified salting-out method (Sunnucks and Hales, 1996) and nebulized for 6 min to obtain 200-600 bp fragments.

Partial genome sequencing was carried out using a Nextera kit in a sixth of an Illumina HiSeq 2000 lane. An initial mitogenome assembly generated by MIRA was used as an input for the MITObim algorithm (Hahn et al., 2013) using default parameters. Mitogenome coverage was obtained using Tablet software (Milne et al., 2013). Mitos WebServer (Bernt et al., 2013) and MitoFish (Iwasaki et al., 2013) were used for annotation. Blast searches (Altschul et al., 1997) against fish amino acid sequences confirmed gene boundaries. tRNA predictions were confirmed using tRNAscan-SE (Lowe and Eddy, 1997). Ribosomal RNA annotations were estimated through automatic analysis provided by Mitos Web Server and MitoFish followed by visual inspection of nucleotide sequence alignments against other Pimelodidae rRNAs.

The complete mitochondrial genome for L. alexandri was assembled using 0.06% (203,036 reads) of the total paired-end reads sequenced (33,839,478 reads of 100 bp each). The assembly provided a circular mitogenome with 134.1 x coverage comprised 16,445 bp, a size similar to the average mitogenome of catfishes. Its gene content also followed the typical pattern for teleost mitogenomes (Prosdocimi et al., 2012, Song et al., 2012, Zhang et al., 2013, Perini et al., 2014), being composed of 37 genes, including 13 protein-coding genes, 22 tRNAs, 2 rRNAs, and 1 non-coding control region (Table S1, Supplementary Material). The mitogenome of Lophiosilurus alexandri is available in GenBank under the accession number KJ494387.

An in-house pipeline developed in Python (https://github.com/igorrcosta/phylomito) was used to: (i) concatenate individual alignments of mitochondrial proteins, (ii) retrotranslate these alignments into codons/nucleotides, and (iii) provide a supermatrix dataset that has been used as input into MEGA 7 for modeltest and phylogeny reconstruction (Kumar et al., 2016).

The phylogenetic relationship between L. alexandri and the other 20 catfishes and two outgroups from the Gymnotiformes and Characiformes orders (Table 1) was recovered using a supermatrix approach of 11,468 nucleotides produced after the concatenation and reverse translation of protein sequence alignments for all the 13 mitochondrial proteins. A maximum likelihood tree was generated using all alignment sites with the best model found by MEGA (GTR+G+I). The phylogenomic analysis produced a consistent tree in accordance with phylogenetic evidence obtained using rag1 and rag2 nuclear genes recovered using 3,660 base pairs (Sullivan et al., 2006). Whole mitochondrial data, however, also evidenced new features, such as (i) a more ancestral split of Amblycipitidae species and also (ii) a highly supported clade (bootstrap=93) grouping families Ictaluridae, Cranogladidae and Pangasidae. L. alexandri, Pimelodus pictus and two species from the genus Pseudoplatystoma were clustered in the same clade with a very confidence support after 1000 resamplings (bootstrap=100) (Figure 1), corroborating the monophyletic relationship of the Pimelodoidea clade, as previously recovered elsewhere (Sullivan et al., 2006). The mitogenome described here is the first representative for the family Pseudopimelodidae.

Table 1 List of species, taxonomic information and accession numbers used in the phylogenetic analyses. 

Order Family Species GenBank ID Size (bp) Reference
Siluriformes Doradidae Amblydoras gonzalezi NC_015745.1 16505 Nakatani et al., 2011
Siluriformes Doradidae Platydoras armatulus NC_025585.1 16470 Liu et al., 2016
Siluriformes Cranoglanididae Cranoglanis bouderius NC_008280.1 16539 Peng et al., 2006
Siluriformes Clariidae Clarias sp. NC_015749.1 16508 Nakatani et al., 2011
Siluriformes Clariidae Clarias fuscus NC_023924.1 16518 Zhou et al., 2015
Siluriformes Ictaluridae Ictalurus punctatus NC_003489.1 16497 Waldbieser et al., 2003
Siluriformes Ictaluridae Ictalurus furcatus NC_028151.1 16499 Liu et al. (Unpublished)
Siluriformes Amblycipitidae Liobagrus marginalis NC_022923.1 16483 Li et al., 2014
Siluriformes Amblycipitidae Liobagrus nigricauda NC_021407.1 16512 Jia et al., 2013b
Siluriformes Amblycipitidae Liobagrus obesus NC_008232.1 16531 Kartavtsev et al., 2007
Siluriformes Pangasiidae Pangasianodon gigas NC_006381.1 16533 Jondeung et al., 2007
Siluriformes Pangasiidae Pangasianodon hypophthalmus NC_021752.1 16522 Zhao et al., 2014
Siluriformes Pangasiidae Pangasius larnaudii NC_015839.1 16471 Nakatani et al., 2011
Siluriformes Pangasiidae Pangasius pangasius NC_023924.1 16476 Mohindra et al., 2015
Siluriformes Siluridae Silurus glanis NC_014261.1 16526 Vitta et al., 2011
Siluriformes Siluridae Silurus meridionalis NC_014866.1 16527 Liang et al., unpublished
Siluriformes Siluridae Pterocryptis conchichinensis NC_027107.1 16501 Xu et al., 2016
Siluriformes Pseudopimelodidae Lophiosilurus alexandri KJ494387 16445 Present work
Siluriformes Pimelodidae Pimelodus pictus NC_015797.1 16575 Nakatani et al., 2011
Siluriformes Pimelodidae Pseudoplatystoma corruscans NC_026846.1 16123 Prosdocimi et al. (Unpublished)
Siluriformes Pimelodidae Pseudoplatystoma magdaleniatum NC_026526.1 16568 Rangel-Medrano et al., 2015
Characiformes Characidae Paracheirodon axelrodi NC_023270.1 17100 Zhang et al., 2014
Gymnotiformes Hypopomidae Brachyhypopomus occidentalis NC_015078.1 16542 Lavoue et al., 2012

Figure 1 Molecular phylogenetic analysis of pacamã, 20 catfishes and two outgroups. A total of 11,468 positions were analyzed consisting in the concatenation of 13 mitochondrial genes. A tree was built using maximum likelihood approaches with GTR+G+I model. Outgroups were used to root the tree. All families and genera of catfishes analyzed were revealed as monophyletic (colored boxes). Bootstrap values (1000 replicates) are shown at the corresponding nodes. 

Acknowledgments

The study received fincancial support from the Brazilian funding agencies FAPERJ (E-26/010.001625/2014 and E-26/202.810/2015) and CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico; fellowship grant 308537/2014-9).

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Supplementary Material

The following online material is available for this article:

Table S1- Mitochondrial genome characteristics of L. alexandri (KJ494387).

Associate Editor: Houtan Noushmehr

Received: January 19, 2016; Accepted: June 20, 2016

Send correspondence to Daniel C. Carvalho. Laboratório de Genética da Conservação, Programa de Pós-Graduação em Biologia dos Vertebrados, Pontifícia Universidade Católica de Minas Gerais (PUC Minas), Av. Dom José Gaspar, 500, Coração Eucarístico 30535-901 - Belo Horizonte, MG, Brazil. Email: danielcarvalho@pucminas.br

*

In memoriam (08/01/2015)

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