Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei

Tanegashima, Chiharu; Nishimura, Osamu; Motone, Fumio; Tatsumi, Kaori; Kadota, Mitsutaka; Kuraku, Shigehiro

doi:10.1038/sdata.2018.200

Cited by 13 publications

(9 citation statements)

References 24 publications

(18 reference statements)

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“…5g-i) are expressed in the posterior regions concomitantly with their sister paralogues in the Hox A, B and D clusters. We further surveyed the transcriptome data of other elasmobranch species 23,24 , which uncovered more Hox C genes of the zebra bullhead shark (Fig. 3k).…”

Section: Evolution Of Hox Genes and Clustersmentioning

confidence: 99%

“…While the determinant of loss or retention of gene duplicates is often imputed to their functions 27 , the effect of intrinsic genomic characteristics, independent of gene functions, has also been proposed as a cause 28 . As the less-derived shark genomes are expected to better reconstruct the differentiation process of ancient gene duplicates, we performed a multi-faceted comparison focusing on 23,24 . Closed pink boxes, presence of intact genes; grey boxes, pseudogenization indicated by a stop codon inside the homeobox (see Supplementary Fig.…”

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

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Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

et al. 2018

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Sequencing the large genomes of sharks. We focused on the brownbanded bamboo shark Chiloscyllium punctatum, for which we recently tabled embryonic stages 8 , and the cloudy catshark Scyliorhinus torazame. Their whole genomes, measured to be approximately 4.7 and 6.7 Gbp, respectively, were sequenced de novo to obtain assemblies including megabase-long scaffolds (Supplementary Note 1.1). We also assembled the genome of the whale shark Rhincodon typus using short sequence reads previously generated 3 (Supplementary Note 1.2). Using these genome assemblies, we performed genome-wide gene prediction, assisted by transcript evidence and protein-level homology to other vertebrates. The obtained genome assemblies and gene models exhibit high coverage (Supplementary Fig. 1), and of these, the bamboo shark genome assembly achieved the highest continuity (N50 scaffold length, 1.9 Mbp) and completeness (97% of reference orthologues identified at least partially). Using the novel gene models, we constructed orthologue groups encompassing a diverse array of vertebrate species (see below). Our products outperform existing

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Section: Evolution Of Hox Genes and Clustersmentioning

confidence: 99%

Section: Nature Ecology and Evolutionmentioning

confidence: 99%

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

et al. 2018

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“…Our current phylogenetic analyses support the loss of VTR2A at the base of extant cartilaginous fishes, with further losses of VTR1B and VTR2B at the base of Elasmobranchii. We searched for the missing genes VTR1B, VTR2A and VTR2B in several available transcriptome assemblies from cartilaginous fish species: the zebra bullhead shark (Heterodontus zebra) (20), ocellate spot skate (Okamejei kenojei) (21), blue shark (Prionace glauca) (22), elephant shark (23), winter skate (Leucoraja ocellata) (24), and small-spotted catshark (Scyliorhinus canicula) (25). However, we could not identify putative VTR1B, VTR2A or VTR2B transcripts in these datasets.…”

Section: Cartilaginous Fishesmentioning

confidence: 99%

The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications

2022

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The neuronal and neuroendocrine peptides oxytocin (OT) and vasotocin (VT), including vasopressins, have six cognate receptors encoded by six receptor subtype genes in jawed vertebrates. The peptides elicit a broad range of responses that are specifically mediated by the receptor subtypes including neuronal functions regulating behavior and hormonal actions on reproduction and water/electrolyte balance. Previously, we have demonstrated that these six receptor subtype genes, which we designated VTR1A, VTR1B, OTR, VTR2A, VTR2B and VTR2C, arose from a syntenic ancestral gene pair, one VTR1/OTR ancestor and one VTR2 ancestor, through the early vertebrate whole-genome duplications (WGD) called 1R and 2R. This was supported by both phylogenetic and chromosomal conserved synteny data. More recently, other studies have focused on confounding factors, such as the OTR/VTR orthologs in cyclostomes, to question this scenario for the origin of the OTR/VTR gene family; proposing instead less parsimonious interpretations involving only one WGD followed by complex series of chromosomal or segmental duplications. Here, we have updated the phylogeny of the OTR/VTR gene family, including a larger number of vertebrate species, and revisited seven representative neighboring gene families from our previous conserved synteny analyses, adding chromosomal information from newer high-coverage genome assemblies from species that occupy key phylogenetic positions: the polypteriform fish reedfish (Erpetoichthys calabaricus), the cartilaginous fish thorny skate (Amblyraja radiata) and a more recent high-quality assembly of the Western clawed frog (Xenopus tropicalis) genome. Our analyses once again add strong support for four-fold symmetry, i.e., chromosome quadruplication in the same time window as the WGD events early in vertebrate evolution, prior to the jawed vertebrate radiation. Thus, the evolution of the OTR/VTR gene family can be most parsimoniously explained by two WGD events giving rise to the six ancestral genes, followed by differential gene losses of VTR2 genes in different lineages. We also argue for more coherence and clarity in the nomenclature of OT/VT receptors, based on the most parsimonious scenario.

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“…The sheared DNA was used for paired-end library preparation with a KAPA LTP Library Preparation Kit (KAPA Biosystems). The optimal numbers of PCR cycles for individual libraries were determined with a Real-Time Library Amplification Kit (KAPA Biosystems) by preliminary qPCR-based quantification using an aliquot of adaptor-ligated DNAs as described previously 24 . Small molecules in the prepared libraries were removed by size selection using Agencourt AMPure XP (Beckman Coulter).…”

Section: Methodsmentioning

confidence: 99%

Inference of a genome-wide protein-coding gene set of the inshore hagfishEptatretus burgeri

Yamaguchi

Hara

Tatsumi

et al. 2020

Preprint

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The group of hagfishes (Myxiniformes) arose from agnathan (jawless vertebrate) lineages and is one of the only two extant cyclostome taxa, together with lampreys (Petromyzontiformes). Even though whole genome sequencing has been achieved for diverse vertebrate taxa, genome-wide sequence information has been highly limited for cyclostomes. Here we sequenced the genome of the inshore hagfish Eptatretus burgeri using DNA extracted from the testis, with a short-read sequencing platform, aiming at reconstructing a high-coverage coding gene catalogue. The obtained genome assembly, scaffolded with mate-pair reads and paired RNA-seq reads, exhibited an N50 scaffold length of 293 Kbp, which allowed the genome-wide prediction of coding genes. This computation resulted in the gene models whose completeness was estimated at the complete coverage of more than 83 % and the partial coverage of more than 93 % by referring to evolutionarily conserved single-copy orthologs. The high contiguity of the assembly and completeness of resulting gene models promises a high utility in various comparative analyses including phylogenomics and phylome exploration.

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Embryonic transcriptome sequencing of the ocellate spot skate Okamejei kenojei

Cited by 13 publications

References 24 publications

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

Shark genomes provide insights into elasmobranch evolution and the origin of vertebrates

The Evolution of Oxytocin and Vasotocin Receptor Genes in Jawed Vertebrates: A Clear Case for Gene Duplications Through Ancestral Whole-Genome Duplications

Inference of a genome-wide protein-coding gene set of the inshore hagfishEptatretus burgeri

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