Complete mitochondrial genome and the phylogenetic position of the smalleye pygmy shark Squaliolus aliae (Squaliformes: Dalatiidae)

Abstract

The complete mitogenome of the smalleye pygmy shark Squaliolus aliae (Squaliformes: Dalatiidae) is presented in this study firstly. It is 16,717 bp with a nucleotide base composition of 30.7% A, 26.2% C, 14.7% G and 28.5% T, containing 37 genes and a control region with typical order as vertebrate. There are 23bp short intergenic spaces and 28bp overlaps locating in gene junctions. 2 rRNA genes are located in heavy strand. Twenty-two tRNA genes range from 67bp (tRNA-Cys) to 75 bp (tRNA-Leu1). Two initial codons (ATG and GTG) and two terminal codons (TAA and T) are found in protein-coding genes. The phylogenetic result shows that S. aliae in this study is clustered to the (Somniosus pacificus + Squalidae).

The smalleye pygmy shark Squaliolus aliae, one of the smallest shark living in deep-water (ranging from 200 to 2000m), belongs to the family Dalattidae in the order Squaliformes (Last & Stevens 1994). It is an ovoviviparous fish characterized by its small eye, mainly feeding on cephalopods and small midwater bony fishes, and often found by people near continental and island land masses in Western Pacific from Japan to Australia (Last & Stevens 1994; Compagno & Niem 1998). We determine the complete mitogenome of S. aliae and construct the phylogenetic tree of Squalimorphs, hoping it can contribute to the molecular and phylogenetic study about sharks.

One specimen of S. aliae, collected by Museum of Marine Biology of Xiamen University (accession number:TW2010051411), was captured from the East China Sea. The experimental protocol and data analysis methods followed Chen et al. (2014). Excluding the outgroup Chimaera monstrosa, all species of Squalimorphs with complete mitogenomes available in the GenBank were selected to construct the phylogenetic tree by the Bayesian method (using three partitions: 12S and 16S rRNA genes, the first and second codons of 12 heavy strand encoded protein genes).

The complete size of the whole mitogenome in S. aliae (Genbank Accession Number: KU873080) is 16,717 bp with a nucleotide base composition of 30.7% A, 26.2% C, 14.7% G and 28.5% T, and this circle molecular has a typical genomic organization and gene order (2 rRNA genes, 22 tRNA genes, 13 protein-coding genes and a non-coding control region) as most vertebrates. 12S rRNA (950bp) and 16S rRNA(1668bp) are both between tRNA-Phe and tRNA-Leu1 genes, separated by tRNA-Val gene, locating in heavy strand. Twemty-two tRNA genes range from 67bp (tRNA-Cys) to 75 bp (tRNA-Leu1), among which although tRNA-Ser2 replaces the dihydrouridine arm by a simple loop, others all can fold into a typical clover-leaf secondary structure. Except CO1 gene that starts with codon GTG, the remaining 12 protein-coding genes all use standard codon ATG as their initial codon. While there is no special case in terminal codon usage, all 13 protein-coding genes are terminated by standard codon TAA/T. Locating in gene junctions, there are 23bp short intergenic spaces and 28bp overlaps. The control region is 1081 bp with a higher A + T (63.1%) than the average value for the whole mitogenome (59.2%).

In the Bayesian tree, all nodes are strongly supported (Figure 1). Each order was monophyletic. The basal division is between Hexanchiformes and the remaining orders (Pristiophoriformes, Squaliformes and Squatiniformes). The Pristiophoriformes is the sister to the Squaliformes. The Squatiniformes is clustered to the (Pristiophoriformes + Squaliformes) clade. Within the order Squaliformes, Somniosus pacificus (Dalatiidae) clusters to the family Squalidae instead of S. aliae, which belongs to the same family as Somniosus pacificus do in the morphological view. Therefore, the relationship within the order Squaliformes needs further study with more species.

Figure 1.

Phylogenetic position of Squaliolus aliae Chimaera monstrosa (AJ310140.1) is selected as the out group. One species from the order Pristiophoriformes is Pristiophorus japonicus (NC_024110.1). Four species from the order Squaliformes are: Somniosus pacificus (NC_022734.1), Squaliolus aliae (KU873080), Cirrhigaleus australis (KJ128289), Squalus acanthias (NC_002012.1). Three species from the order Squatiniformes are: Squatina japonica (NC_024276), S. nebulosa (NC_025578.1), S. formosa (KM084865). Five species from the order Hexanchiformes are: Chlamydoselachus anguineus (NC_022729), Heptranchias perlo (NC_022730), Hexanchus griseus (KF894491), H. nakamurai (AB560491) Notorynchus cepedianus (NC_022731).

Disclosure statement

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

Funding information

This study is supported by Ministry of Science and Technology of Zhejiang Province (2013F50015).