Complete mitochondrial genome sequence of neotropical fish Astyanax giton Eigenmann 1908 (Ostariophysi; Characidae)

Abstract

Here we report, for the first time, the complete mitochondrial genome of Astyanax giton which, together with other species, are popularly known as tetras. The mitogenome’s length is 16,643 bp, containing 13 protein-encoding genes (CDS), two ribosomal RNAs (rRNA), 22 RNA transfer (tRNA) and one control region (D-loop). As for other vertebrates, all genes are encoded on the heavy strand except for ND6 and eight tRNA genes. In the phylogenetic analyses, this species and other Astyanax were paraphyletic.

In the Characidae family, the genus Astyanax is a taxon that encompasses species with poorly known phylogenetic kinships, popularly known as tetras. It currently comprises 146 valid species with a wide distribution on the Neotropical region (Lima et al. 2003), occurring from the southern United States to northern Argentina (Froese and Pauly 2011). The taxonomy of the Astyanax genus is still unsettled, although morphological (Mirande 2009) and molecular data (Javonillo et al. 2010) indicate that this taxon is paraphyletic. Until the present date, only two mitogenomes of the genus Astyanax have been described, which underlines the relevance of the description of the complete mitogenome of Astyanax giton.

Astyanax giton was collected in the Doce River Basin, at the headwaters of the Latão Stream, in the city of Coimbra (20°49′66″S, 42°49′58″W) in the state of Minas Gerais, in southeastern Brazil. The voucher specimen was deposited in the scientific collection of the Museum of Zoology João Moojen, at the Federal University of Viçosa, Minas Gerais, Brazil (voucher no. CT2205). This work was carried out with DNA purified from the muscle tissue and the genomic library was sequenced with 2 × 300 bp paired-end reads using the Illumina MiSeq (Illumina Inc., San Diego, CA). The quality of the sequencing was evaluated using FASTQC v.0.11.5 and the reads were trimmed (Q20 score) and filtered by size (75 nt) using Trimmomatic v0.33 (Bolger et al. 2014). The mitogenome of A. giton was assembled using a de novo assembly in CLC Genomics Workbench v6.5.1 (CLC Bio, Boston, MA). The mitogenome sequence was selected and annotated using MitoAnnotator (Iwasaki et al. 2013).

The mitogenome of A. giton is typical of vertebrates (Boore 1999) and its length was 16,643 bp (GenBank access no. MF805815), with a 121-fold coverage. Thirty-seven genes were functionally annotated, 13 coding DNA sequences (CDS), two ribosomal RNA (rRNA), 22 transfer RNAs (tRNA) and a control region (D-loop) of 997 bp. Most of the genes are located on the heavy strand (H), except for eight tRNAs and ND6. Besides the D-loop region, A. giton has 14 intergenic regions in its mitogenome, which add up to 94 bp in length.

The 13 CDS of A. giton represent 68.6% of the total mitogenome. The COI and ND3 genes start with the GTG codon, whereas others show usual ATG codon. Three of the 13 CDS contain the TAA stop codon (ND1, ND4L and ND6); five the incomplete T- stop codon (COII, ATPase6, COIII, ND3 and ND4); three the TAG stop codon (ND2, ATPase8 and CYTB) and finally, two had the AGG stop codon (COI and ND5).

Mitogenomes of the Characidae species available at NCBI were aligned and the phylogeny reconstruction was done using the Bayesian inference (BI) and maximum-likelihood (ML) methods, using the GTR + I + G model, with Acestrorhynchus sp. as outgroup (Figure 1). In the phylogenetic analysis, the genus Astyanax was considered paraphyletic, with A. giton as a sister group of ((Astyanax paranae, Astyanax mexicanus) Grundulus bogotensis).

Figure 1.

Bayesian phylogenetic tree for Characidae mitogenomes using Acestrorhynchidae as outgroup. Numbers at each node represent the posterior probability (PP) obtained in Bayesian (BI) analysis, and percentage of bootstrap values (BV) obtained using Maximum Likelihood (ML) analysis. Asterisks represent nodes that were not retrieved using ML analysis. In the ML analysis, clade consistency was verified using 1000 pseudoreplicates obtained with the ultrafast bootstrap method; BI analysis was performed using four independent chains with 10,000,000 generations and the first 25% of the generations were discarded as burn-in.

Disclosure statement

The authors report no conflicts of interest. The authors alone are responsible for the content and writing of the paper.