Dataset Information

The phylogenomic position of the smooth lanternshark Etmopterus pusillus (Squaliformes: Etmopteridae) inferred from the mitochondrial genome.

ABSTRACT: In this study, the complete mitogenome of the Smooth lanternshark Etmopterus pusillus (Squaliformes: Etmopteridae) was firstly determined. It was 16,729 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 1 putative control region with typical order to that of most other vertebrates. Its nucleotide base composition is 31.3% A, 23.0% C, 14.3% G and 31.5% T. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes. The phylogenetic results showed that E. pusillus was clustered to Squaliolus aliae (Dalatiidae) and suggested that Dalatiidae was polyphyletic.

SUBMITTER: Chen H

PROVIDER: S-EPMC7875202 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

The phylogenomic position of the smooth lanternshark <i>Etmopterus pusillus</i> (Squaliformes: Etmopteridae) inferred from the mitochondrial genome.

Chen Hao H Chen Xiao X Gu Xichun X Wan Huantong H Chen Xi X Ai Weiming W

Mitochondrial DNA. Part B, Resources 20160419 1

In this study, the complete mitogenome of the Smooth lanternshark <i>Etmopterus pusillus</i> (Squaliformes: Etmopteridae) was firstly determined. It was 16,729 bp, consisting of 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes and 1 putative control region with typical order to that of most other vertebrates. Its nucleotide base composition is 31.3% A, 23.0% C, 14.3% G and 31.5% T. Two start codons (GTG and ATG) and two stop codons (TAG and TAA/T) were used in the protein-coding genes ...[more]

PMID: 34395874

Similar Datasets

Project description:The velvet belly lanternshark (Etmopterus spinax) is a small deep-sea shark commonly found in the Eastern Atlantic and the Mediterranean Sea. This bioluminescent species is able to emit a blue-green ventral glow used in counter-illumination camouflage, mainly. In this study, paired-end Illumina HiSeqTM technology has been employed to generate transcriptome data from eye and ventral skin tissues of the lanternshark. About 64 and 49 million Illumina reads were generated from skin and eye tissues respectively. The assembly allowed us to predict 119,749 total unigenes including 94,569 for the skin transcriptome and 94,365 for the eye transcriptome while 74,753 were commonly found in both transcriptomes. A taxonomy filtering was applied to extract a reference transcriptome containing 104,390 unigenes among which 38,836 showed significant similarities to known sequences in NCBI non-redundant protein sequences database. Around 58% of the annotated unigenes match with predicted genes from the Elephant shark (Callorhinchus milii) genome. The transcriptome completeness has been evaluated by successfully capturing around 98% of orthologous genes of the « Core eukaryotic gene dataset » within the E. spinax reference transcriptome. We identified potential "light-interacting toolkit" genes including multiple genes related to ocular and extraocular light perception processes such as opsins, phototransduction actors or crystallins. Comparative gene expression analysis reveals eye-specific expression of opsins, ciliary phototransduction actors, crystallins and vertebrate retinoid pathway actors. In particular, mRNAs from a single rhodopsin gene and its potentially associated peropsin were detected in the eye transcriptome, only, confirming a monochromatic vision of the lanternshark. Encephalopsin mRNAs were mainly detected in the ventral skin transcriptome. In parallel, immunolocalization of the encephalopsin within the ventral skin of the shark suggests a functional relation with the photophores, i.e. epidermal light-producing organs. We hypothesize that extraocular photoreception might be involved in the bioluminescence control possibly acting on the shutter opening and/or the photocyte activity itself. The newly generated reference transcriptome provides a valuable resource for further understanding of the shark biology.

Project description:BackgroundThe lancelet Asymmetron inferum (subphylum Cephalochordata) was recently discovered on the ocean floor off the southwest coast of Japan at a depth of 229 m, in an anaerobic and sulfide-rich environment caused by decomposing bodies of the sperm whale Physeter macrocephalus. This deep sulfide-rich habitat of A. inferum is unique among the lancelets. The distinguishing adaptation of this species to such an extraordinary habitat can be considered in a phylogenetic framework. As the first step of reconstruction of the evolutionary processes in this species, we investigated its phylogenetic position based on 11 whole mitochondrial genome sequences including the newly determined ones of the whale-fall lancelet A. inferum and two coral-reef congeners.ResultsOur phylogenetic analyses showed that extant lancelets are clustered into two major clades, the Asymmetron clade and the Epigonichthys + Branchiostoma clade. A. inferum was in the former and placed in the sister group to A. lucayanum complex. The divergence time between A. inferum and A. lucayanum complex was estimated to be 115 Mya using the penalized likelihood (PL) method or 97 Mya using the nonparametric rate smoothing (NPRS) method (the middle Cretaceous). These are far older than the first appearance of large whales (the middle Eocene, 40 Mya). We also discovered that A. inferum mitogenome (mitochondrial genome) has been subjected to large-scale gene rearrangements, one feature of rearrangements being unique among the lancelets and two features shared with A. lucayanum complex.ConclusionOur study supports the monophyly of genus Asymmetron assumed on the basis of the morphological characters. Furthermore, the features of the A. inferum mitogenome expand our knowledge of variation within cephalochordate mitogenomes, adding a new case of transposition and inversion of the trnQ gene. Our divergence time estimation suggests that A. inferum remained a member of the Mesozoic and the early Cenozoic large vertebrate-fall communities before shifting to become a whale-fall specialist.

Dataset Information

The phylogenomic position of the smooth lanternshark Etmopterus pusillus (Squaliformes: Etmopteridae) inferred from the mitochondrial genome.

Publications

The phylogenomic position of the smooth lanternshark <i>Etmopterus pusillus</i> (Squaliformes: Etmopteridae) inferred from the mitochondrial genome.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets