The complete mitochondrial genome of Gephyrocharax atracaudatus (Characiformes, Characidae) and phylogenetic studies of Characiformes

Abstract

Here, we report the complete mitochondrial genome sequence of Gephyrocharax atracaudatus. The genome is found to be 17,049 bp in length and has a base composition of A (29.95%), G (15.29%), C (26.13%) and T (28.63%). Similar to other Gephyrocharax species, it contains a typically conserved structure including 13 protein-coding genes, 2 rRNA genes, 1 control region (D-loop) and 22tRNA genes. The proportion of coding sequences with a total length of 11,420 bp is 66.98%, which encodes 3800 amino acids. All protein-coding genes started with Met, ND1, ND2, ND3, ND4L, ND5 and CytB ended by TAA as a stop codon, CO1 ended by AGG as a stop codon, CO2, ATP6, ND4 ended by a single T, ATP8, ND5 ended by TAG as a stop codon and CO3 ended by TA as a stop codon. The lengths of 12S ribosomal RNA and 16S ribosomal RNA are 950 bp and 1682 bp, respectively. The length of control region is 1396 bp, ranging from 15,653 bp to 17,049 bp. The complete mitochondrial genome sequence provided here would be useful for further understanding the evolution of ratite and conservation genetics of Gephyrocharax atracaudatus.

Keywords:

• Gephyrocharax atracaudatus
• mitochondrial genome
• evolutionary relationships

Gephyrocharax atracaudatus, belongs to the family Gephyrocharax, Characiformes, is a subtropical fish which distributes in the Panama, Province Cerro-Azul and former Canal Zone, Frijoles River basin of Central America (Weitzman and Fink 1985). Although two complete mitochondrial (mt) genomes belonging to Gephyrocharax atracaudatus have been determined, the Gephyrocharax atracaudatus mt genome sequence has not been reported yet.

Here, we sequenced and characterised the complete mt genome of Gephyrocharax atracaudatus. The specimen was collected from Flamenco Island, Panama (9°2′7″N, 79°28′43″W) and stored in a refrigerator of –80 °C in Zhejiang Engineering Research Center for Mariculture and Fishery Enhancement Museum. Total genomic DNA was extracted from muscle tissue of individual using the phenol-chloroform method (Barnett and Larson 2012). The calculation of base composition and phylogenetic construction were conducted by MEGA6.0 software (Tamura et al. 2013). The transfer RNA (tRNA) genes were generated using the program tRNAs-can-SE (Lowe and Eddy 1997). The mt genome sequence of Gephyrocharax atracaudatus with the annotated genes was deposited in GenBank with the accession number of MH636341.

Similar to the typical mitogenome of vertebrates, the mitogenome of Gephyrocharax atracaudatus is a closed double-stranded circular molecule of 17,049 nucleotides (GenBank accession No. MH636341), which contains 13 protein-coding genes, 2 ribosomal RNA genes, 22 tRNA genes and 2 main non-coding regions (Boore 1999; Zhu, Gong, et al. 2018; Zhu, Lü, et al. 2018). The contents of A, G, T and C are 29.95%, 15.29%, 28.63% and 26.13%, respectively. Most mitochondrial genes are encoded on H-strand except for ND6 and eight tRNA genes (Gln, Ala, Asn, Cys, Tyr, Ser, Glu and Pro), which are encoded on the L-strand. The proportion of coding sequences with a total length of 11,420 bp is 66.98%, 13 protein-coding (PCGs) genes encode 3800 amino acids in total. All the protein-coding genes use the initiation codon ATG except COI uses GTG, which is quite common in vertebrate mtDNA (Miya et al. 2001; Liu et al. 2016). ND1, ND2, ND3, ND4L, ND5, CytB ended by TAA as a stop codon, CO1 ended by AGG as a stop codon, CO2, ATP 6, ND4 ended by T as a stop codon, ATP8, ND5 ended by TAG as a stop codon, CO3 ended by TA as a stop codon. The 12S rRNA and 16S rRNA are 950 and 1682 bp, which are both located in the typical positions between tRNA-Phe and tRNA-Leu (UUA), separated by tRNA-Val. The origin of light-strand replication is located in a cluster of five tRNA genes (WANCY) as in other vertebrates (Petrillo et al. 2006), The length of control region is 1396 bp, ranging from 15,653 bp to 17,049 bp.

Phylogenetic analysis included mt genome of Gephyrocharax atracaudatus and the other 14 species that are from the order Chalceus, Paracheirodon, Carnegiella, Chilodus, Lebiasina and others, which belong to Characiformes. The results of the present study support that Gephyrocharax atracaudatus has a closest relationship with Hasemania nana, which was highly supported by a bootstrap value of 99 (Figure 1).

Figure 1. Phylogenetic tree derived from NJ based on concatenated nucleotide sequences of twelve PCGs. Including Gephyrocharax atracaudatus, Chalceus macrolepidotus, Paracheirodon axelrodi, Carnegiella strigata, Chilodus punctatus, Lebiasina astrigata, Piaractus sp, Grundulus bogotensis, Ichthyoelephas longirostris, Paracheirodon innesi, Paracheirodon innesi, Brycon orbignyanus, Hasemania nana, Grundulus bogotensis, Hemigrammus bleheri and Astyanax paranae.

Disclosure statement

No potential conflict of interest was reported by the authors.