A new gene order in the mitochondrial genome of the deep-sea diaphanous hatchet fish Sternoptyx diaphana Hermann, 1781 (Stomiiformes: Sternoptychidae)

Abstract

Species of the Sternoptychidae teleost family display an impressive morphology, including their extreme reduced size. Here, we report the first mitochondrial genome of the diaphanous hatchet fish Sternoptyx diaphana. By using short-read sequencing Illumina HiSeq, we generated two mitochondrial contigs which were later physically assembled by PCR. The mitochondrial genome of S. diaphana was 17,224 bp in length (excluding the control region) and is composed of 13 PCGs and 2 ribosomal RNA genes. Strikingly, we could not identify the tRNA-Phe and two copies of tRNA-Met were differently positioned. Additionally, the mitogenome displays a completely new gene rearrangement among vertebrates. We expect that the study presented here will pave the way for further molecular studies with this underrepresented group of illusive teleost fish.

Complete mitogenomes of four Trichiurus species: A taxonomic review of the T. lepturus species complex

“…Overall, the mitogenomes of four Trichiurus species in the present study have a gene order and composition similar to other Trichiurus mitogenomes in previous studies (e.g., Liu and Cui 2009;Liu et al 2013;Zheng et al 2019;Mukundan et al 2020). The gene order of the mitogenomes in Trichiuridae was similar to that in most teleosts, although different types of gene rearrangements were observed within Pleuronectiformes (Gong et al 2015) and Stomiiformes (Arrondo et al 2020).…”

The complete mitogenome of Halictus (Seladonia) aerarius (Hymenoptera: Halictidae) and phylogenetic analysis

“…The complete mitogenome of S. aeraria is 15, 410 bp in length with 18.1% GC content. It contained 13 PCGs, 22 tRNA, two rRNAs and a hypothetical control region (CR), which was consistent with the general composition of invertebrate mitogenome (Li et al 2020 ). The start codons of all PCGs are ATA for nad2 ; ATC for atp8 ; ATG for atp6 , cox3 , cytb , nad4 , nad6 and ATT for cox1 , cox2 , nad1, nad3, nad4L , nad5 .…”

Mitochondrial replication's role in vertebrate mtDNA strand asymmetry

“…The difficulty in resolving these repetitive regions using short reads prevented the assembly of a single contig in A. olfersii (composed of two contigs), as well as the circularization of the A. hemigymnus assembly. This factor also hampered the assembly of the recently published S. diaphana mtDNA, which required scaffolding with Sanger sequencing [ 16 ]. Nevertheless, we efficiently identified the CSB-II (thus the CR) in all but one (i.e.…”

“…We next analysed the phylogenetic relationships between the various deep-sea hatchetfish species. The resulting phylogenetic inference, rooted with Coregonus lavaretus (Linnaeus, 1758) (following [ 16 , 30 ]), is split into two major groups, one composed of order Stomiiformes and the other composed of families Synodontidae, Ateleopodidae, Myctophidae and Trachipteridae ( figure 4 ). Stomiiformes' phylogenetic relationships are poorly resolved, with very low support in most of the nodes.…”

“…movement to a distinct location maintaining the genes encoded strand; and the rarest event 'inversion', i.e. genes (or noncoding unities) switch to their complementary strand [1,[12][13][14][15][16][17]. Inversions, when acting upon the replication controlling unities (i.e.…”