The first complete mitochondrial genome of Zu cristatus (Bonelli, 1819) sheds new light on its phylogenetic position and molecular evolution

Abstract

Background: Fishes are key components of the megafauna of the deep sea, and evolutionary adaptations to deep-sea life appear to have occurred independently in at least 22 fish orders. In this context, the analysis of even more fish genomes and mitogenomes has fundamental importance, providing a valuable resource for understanding the molecular mechanisms underlying evolutionary adaptation, especially to extreme environments such as the deep sea. Here, we report the first complete mitochondrial genome of Zu cristatus (Bonelli, 1819), providing essential information on its structure and phylogeny.

Results: After sequencing on the Illumina HiSeq 4000 platform, processing, and assembly via MitoFinder software v.1.4.1, a single circular mtDNA molecule of 17,450 bp in length was annotated. A total of 37 genes were identified, including the first D-loop region for this species. The asymmetry for both AT skews and GC skews is negative, and the AT content is 56.4%. We also detected the presence of 15 small, noncoding, intergenic nucleotide (IGN) regions and some rare stop codons in bony fishes. Pairwise distance and phylogenetic analyses against a list of other mitochondrial sequences from 42 bony fishes confirmed the current phylogeny with previously related orders. EasycodeML analysis revealed that only 4 PCGs underwent positive selection. New questions about the phylogeny of Lampriformes emerged from our phylogenetic analyses of Lampriformes COI.

Conclusion: Overall, the findings of this study highlight the need to elucidate the genetic features of bony fishes in relation to their deep-sea adaptation, with a focus on rare and interesting species.

Keywords: Deep-sea environment; Genome sequencing; Lampriformes; Marine genomics; Marine zoology; Scalloped ribbonfish.

Fig. 1

Map of the catch area of the Z. cristatus with the highlighted point in the Ionian Sea (red star) (36°50’05” N 15°16’49” E). In the red box the Z. cristatus adult specimens analyzed in this study. Images were taken at the Messina University laboratory before the necroscopy of the fish

Fig. 2

Structure of the mitochondrial genome of Z. cristatus isolated in this study. A total of 37 genes (22 tRNAs, 13 protein-coding genes and 2 rRNAs), including the D-loop region, were identified in the genome assembly. The internal circle represents the G + C content per 5 bp (darker lines represent higher G + C contents). The external circle represents the two mtDNA strands (H eternally, L internally). The red, black and avana blocks indicate tRNAs, PCGs, and rRNAs, respectively. The D-loop region is colored brown. The graphical representation of the genome was created via Mitofish, and the Z. cristatus illustration was created via Dr. Serena Savoca

Fig. 3

(A) Information on the AT content (%) of Z. cristatus mitogenome genes. This figure was generated via GraphPad Prism 8.0.1 [121]. (B) Relative synonymous codon usage (RSCU) analysis of the Z. cristatus mitogenome. The RSCU values are represented on the y-axis, and families of synonymous codons and their respective amino acids are indicated on the x-axis. This figure was generated via GraphPad Prism 8.0.1 [121]. C) AT- and GC-skew values of the Z. cristatus whole mitogenome; PCGs concatenated and singularly concatenated; tRNAs, rRNAs and D-loops. This figure was generated via GraphPad Prism 8.0.1 [121]

Fig. 4

Maximum likelihood tree of mitogenomes belonging to 42 fish species generated via RAxML software. The members of the family Trachipteridae were highlighted in green; the members of the family Lampridae were highlighted in yellow; the members of the family Regalecidae were highlighted in red

Fig. 5

Overall mean p-genetic distance ±SD in the PCG comparison of Z. cristatus and the other 42 species selected. The number of base substitutions per site from the average over all sequence pairs is shown. The p-distances are on the y-axis, whereas single PCGs are on the x-axis. Circles and asterisks identify the outliers

Fig. 6

Unrooted radiation tree illustrating the phylogenetic relationships of Lampriformes species based on the currently available mt-co1 sequences. The scale bar corresponds to an estimated evolutionary distance of 0.1. The tree was generated via the iTOL utility. The members of the family Trachipteridae were highlighted in green; the members of the family Lampridae were highlighted in yellow; the members of the family Regalecidae were highlighted in red

Fig. 7

Unrooted radiation tree inferred via JolyTree via 43 mitogenomes downloaded from the MitoFish database (Supplementary Table 2). The scale bar corresponds to an estimated evolutionary distance of 0.1. The tree was generated via the iTOL utility. The members of the family Trachipteridae were highlighted in green; the members of the family Lampridae were highlighted in yellow; the members of the family Regalecidae were highlighted in red; the members of the family Lophotidae were highlighted in light blue; the members of the family Veliferidae were highlighted in orange