Pimelodus maculatus (Siluriformes, Pimelodidae): complete mtDNA sequence of an economically important fish from the São Francisco river basin

Abstract

Pimelodus maculatus is an important commercial fish found in the São Francisco and Paraná river basins. NGS was used to sequence the mtDNA of P. maculatus. The mtDNA was annotated and aligned with that of 25 other fish species to enable phylogenetic analysis. The complete mtDNA molecule had 16,561 bp and its GC content was 43.7%; the structure was similar to that of other vertebrates: 2 rRNA, 22 tRNA, 13 protein-coding genes, and a D-loop region containing 914 bp. Phylogenetic analysis yielded a tree with a high bootstrap coefficient that was coherent with the actual phylogeny of the species.

Keywords: Complete mtDNA; Pimelodus maculatus; next-generation sequencing; ‘mandi’; ‘yellow-mandi catfish’.

Figure 1.

Molecular phylogenetic analysis inferred using the maximum likelihood method based on the Tamura–Nei model (Tamura & Nei 1993) with 1000 bootstrap replications. The analysis was carried out using complete mtDNA of Pimelodus maculatus (GenBank accession no. KX371345) and complete mtDNA of 25 other species: Leiocassis longirostris (GU596454.1), Tachysurus albomarginatus (KF514425.1), Tachysurus brevicaudatus (JX867256.1), Tachysurus vachellii (KT202282.1), Tachysurus eupogon (KJ001784.1), Tachysurus ussuriensis (JX867258.1), Coreobagrus brevicorpus (HM355585.1), Tachysurus tokiensis (AB054127.1), Hemibagrus spilopterus (JQ343983.1), Pangasianodon gigas (AY762971.1), Pangasianodon hypophthalmus (KC846907.1), Pangasius larnaudii (AP012018.1), Pangasius pangasius (KC572135.1), Lophiosilurus alexandri (KT990219), Pseudoplatystoma corruscans (KJ502112.1), Pimelodus pictus (AP012019.1), Platydoras armatulus (KM576101.1), Clarias fuscus (KM029965.1), Clarias gariepinus (KT001082.1), Pterocryptis cochinchinensis (KR028479.1), Silurus glanis (AM398435.2), Silurus asotus (JX256247.1), Silurus meridionalis (JX087350.1), and Prochilodus lineatus (KM245045.1). The phylogenetic tree with the highest log likelihood is shown, with the percentages of trees in which associated taxa clustered together shown next to the branches. The phylogenetic tree was rooted with P. lineatus (Characiformes, Prochilodontidae). The D-loop region was excluded from this analysis because it is considered to be highly variable (Gonder et al. 2007). The phylogenetic tree obtained was coherent with the phylogenetic studies of Sullivan et al. (2006, 2013) and Lundberg et al. (2011), which grouped species in their respective families; Pimelodidae and Pseudopimelodidae were grouped together in the superfamily Pimelodoidea. The analyses were conducted using MEGA7 software (Kumar et al. 2016).