Complete Mitochondrial Genomes of Nannostomus Pencilfish: Genome Characterization and Phylogenetic Analysis

Abstract

Although the pencilfish is a globally popular economic fish in the aquarium market, its taxonomic classification could be further refined. In order to understand the taxonomy of species of the genus Nannostomus (Characiformes, Lebiasinidae) and their phylogenetic position within the order Characiformes, in this study, we characterized mitochondrial genomes (mitogenomes) from four Nannostomus species for the first time. The four mitogenomes exhibited the typical circular structure, with overall sizes varying from 16,661 bp to 16,690 bp. They contained 13 protein-coding genes (PCGs), 2 ribosomal RNA genes (rRNAs), 22 transfer RNA genes (tRNAs), and 1 control region (CR). Nucleotide composition analysis suggested that the mitochondrial sequences were biased toward A and T. Bayesian inference and maximum likelihood analyses based on PCGs support the family Lebiasinidae classification, described using four Nannostomus species, clustering together with Lebiasina multimaculata from the same family. The results of this study support the current taxonomic classification of the family Lebiasinidae. Phylogenetic analysis also suggested that gene rearrangement would not significantly impact the phylogenetic relationships within the order Characiformes. These results might provide new data regarding the phylogeny and classification of the order Characiformes, thus providing a theoretical basis for the economic development of aquarium fish markets.

Keywords: Nannostomus; aquarium fish; mitochondrial genomes; pencilfish; phylogenetic analysis.

Figure 1

Mitogenomes of Nannostomus beckfordi (a), Nannostomus marilynae (b), Nannostomus marginatus (c), and Nannostomus unifasciatus (d). Yellow blocks: CR, green blocks: rRNAs, light purple blocks: tRNAs, dark purple blocks: PCGs.

Figure 2

Nucleotide composition of various datasets of mitogenomes. Hierarchical clustering of Lebiasinidae species (y-axis) based on the content (a) and skewness (b).

Figure 3

A+T content vs. AT-skew in the 48 mitogenomes of the order Characiformes. (a) Total genome; (b) PCGs; (c) tRNAs; (d) rRNAs.

Figure 4

Initiation codon (a) and termination codon (b) usage for the mitochondrial genome protein-coding genes of 48 Characiformes species.

Figure 5

RSCUs of three species of Nannostomus; the termination codon is not included.

Figure 6

Ka/Ks values for the 13 PCGs of four Nannostomus mitogenomes.

Figure 7

The organization of the control region in five Lebiasinidae mitochondrial genomes. The colored ovals indicate the tandem repeats; the remaining regions are shown with green boxes.

Figure 8

The BI (a) and ML (b) phylogenetic trees based on the nucleotide datasets for 13 PCGs from the mitogenomes of 49 species, with the common gene order and rearrangement within Characiformes (yellow boxes indicate the events of gene rearrangement).