http://informahealthcare.com/mdn ISSN: 1940-1736 (print), 1940-1744 (electronic) Mitochondrial DNA, Early Online: 1–2 ! 2015 Universidade Federal De Minas Gerais. DOI: 10.3109/19401736.2015.1053125
MITOGENOME ANNOUNCEMENT
Description and comparison of two economically important fish species mitogenomes: Prochilodus argenteus and Prochilodus costatus (Characiformes, Prochilodontidae)
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Aline Torres de Azevedo Chagas, Anderson Oliveira Carmo, Maı´sa Aparecida Costa, Leonardo Cardoso Resende, Pedro Ferreira Pinto Branda˜o Dias, Ana Paula Vimieiro Martins, and Evanguedes Kalapothakis Departamento de Biologia Geral, Instituto de Cieˆncias Biolo´gicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
Abstract
Keywords
Prochilodus spp. are important Brazilian freshwater migratory fishes with substantial economic and ecological importance. Prochilodus argenteus and Prochilodus costatus are morphologically similar and a molecular species delimitation is impaired due to high degree of sequence identity among the available genetic markers. Here, the complete mitochondrial genome of P. argenteus and P. costatus and their comparison to the mitogenome of P. lineatus are described. The three species displayed a similar mtDNA annotation. A phylogenetic analysis was performed with other Characiformes species. The genus Prochilodus was recovered as a monophyletic group, as well as the family Prochilodontidae, both with high bootstrap probability.
Complete mtDNA, curimba, curimba-pacu, curimba-pioa, next-generation sequencing
Prochilodontidae (Characiformes, Anostomidae) is an important fish family, with great importance for local fisheries and ecology in South American rivers, where it also plays a key role in nutrient cycling (Taylor et al., 2006). In the southeastern region of Brazil, three species can be highlighted: Prochilodus argenteus, Prochilodus costatus, and Prochilodus lineatus. They are detritivorous species whose reproductive period matches with the rainy season when fishes perform long distance migrations upstream for spawning (Sato & Godinho, 2003). P. argenteus (Agassiz, 1829), or ‘‘curimba-pacu’’ is endemic to the Sa˜o Francisco River Basin, where it is sympatric with the also endemic P. costatus (Valenciennes, 1850), known as ‘‘curimba-pioa’’. Together, P. argenteus and P. costatus represent about 50% of total fish catch in some regions where it occurs (Sato & Godinho, 2003). Prochilodus lineatus (Valenciennes, 1836), commonly known as ‘‘curimba’’, naturally inhabits the Parana´-Paraguai and the Paraı´ba do Sul River Basins. It was the only member of genus Prochilodus with fully characterized mitogenome until now (Carmo et al., 2014). Morphologically similar, the three species are distinguished by the number of horizontal rows of scales between dorsal-fin origin and lateral line (Castro & Vari, 2003). Regarding molecular identification, there are a few partial sequences of Cox1 gene available at BOLD (Barcode of Life Databases), but they are insufficient for an identification at species level, given their Correspondence: Evanguedes Kalapothakis, Departamento de Biologia Geral, Instituto de Cieˆncias Biolo´gicas, Universidade Federal de Minas Gerais, Avenida Presidente Antoˆnio Carlos, 6627, Pampulha, Belo Horizonte MG 31270-901, Brazil. Tel: +55 31 3409 2701. Fax: +55 31 3409 2713. E-mail:
[email protected]
History Received 13 May 2015 Accepted 17 May 2015 Published online 14 July 2015
high similarity. Thus, the knowledge of their complete mitochondrial sequences is an important tool for developing of new molecular markers with better resolution at species level. The present work was carried out with DNA purified from the muscle tissue of single specimens of P. argenteus and P. costatus collected in the Paraopeba River, Minas Gerais, Brazil (18 520 23.900 S, 44 460 52.800 W). The samples were stored at the UFMG-BDT Bank of the Federal University of Minas Gerais (deposit codes: UFMG-BDT-PP000001 for P. argenteus and UFMG-BDT-PP000002 for P. costatus). For each species, a genomic library was constructed and sequenced with MiSeq (Illumina Inc., San Diego, CA) technology using a paired-end 300 bp strategy. The assembly was done using Mira 4.0 (Chevreux et al., 1999). The mitochondrial genome of P. argenteus is 16,697 bp length (GenBank accession no. KR014816), solved with 378 coverage. Prochilodus costatus’ mitogenome is 16,699 bp length (KR014817), solved with 345 coverage. For both species, as in P. lineatus, GC content is 44%, with individual base frequencies of 30% A, 16% G, 26% T, and 29% C. Both genomes were annotated using MitoFish webserver (Iwasaki et al., 2013) and contain 2 rRNA, 22 tRNA, and 13 protein-coding genes (PCGs). Gene arrangement and coding-strand data for P. argenteus and P. costatus were according to a typical vertebrate mitogenome and their annotation was very similar to P. lineatus, except for the 12S gene and D-loop region that were 1 pb shorter in P. argenteus. Also, the presence of overlapping coding sequences, most of which overlapped by a single base, is consistent among the three species. Other characteristics are conserved: only Cox1 gene started with GTG codon, and all other PCGs displayed the usual ATG start codon. Six of the 13 PCGs contained a TAA stop codon (Nd1, Cox1, Atp8, Nd4L, Nd5, and Nd6); five displayed the T– – incomplete stop codon (Nd2, Cox2, Nd3, Nd4, and Cytb);
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Figure 1. Phylogenetic analyses were conducted for Prochilodus argenteus (GenBank accession no. KR014816), Prochilodus costatus (KR014817), Prochilodus lineatus (KM245045), Ichthyoelephas longirostris (KP025763), Curimata mivartii (KP025764), Leporinus piavussu (KM886569), Leporinus affinis (AP011994), Hemiodopsis gracilis (AP011990), Piaractus mesopotamicus (KM245046), Pygocentrus nattereri (AP012000) and Myleus sp. (AP011997). The tree was rooted to Pimelodus pictus (AP012019).
and two displayed the TA– incomplete stop codon (Atp6 and Cox3). The differences in the nucleotide composition were evaluated using the CGView Comparison Tool (Grant et al., 2012) that revealed 496% of identity between the sequences of P. lineatus and P. argenteus, 498% of identity between the sequences of P. lineatus and P. costatus, and 496% of identity between the sequences of P. argenteus and P. costatus. D-loop region was the most variable among the three species and, consequently, a suitable target sequence for comparative studies that aim to perform an identification at species level. For phylogenetic analyses, a search was run in the MitoFish webserver for the mitogenomes sequences most similar to P. argenteus and P. costatus. Nine South-American Characiformes species were selected and the tree was rooted to a Siluriformes species. Phylogenetic analyses were conducted using MEGA version 6 (MEGA Inc., Englewood, NJ) (Tamura et al., 2013). Species mitogenomes were aligned and the phylogeny reconstruction was done using a maximum likelihood method and bootstrap analysis with 1000 replications. Due to its hyper varibability, D-loop region was excluded from phylogenetic analysis (Gonder et al., 2007). A relatively well-resolved tree was built, with most of the internal branches supported by moderate to high (70–100%) bootstrap probability (BSPs) (Figure 1). Genus Prochilodus was confidently recovered as a monophyletic group as well as the family Prochilodontidae (BSP ¼ 100%). Superfamily Anostomoidea (Vari, 1983) was also recovered as a monophyletic group, but with lower BSP (69%).
Declaration of interest The authors report no conflicts of interest. This study was supported by CEMIG (Projects GT455 Agreement number 4020000572), Peixe Vivo (Contract number 4570011274/510), and CAPES (Process 23038.006839/ 2014-33).
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