SkateBase, an elasmobranch genome project and collection of molecular resources for chondrichthyan fishes.
TL;DR: This study summarizes available data for chondrichthyes and describes resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate, serving as the skate genome project portal linking data, research tools, and teaching resources.
Abstract: Chondrichthyan fishes are a diverse class of gnathostomes that provide a valuable perspective on fundamental characteristics shared by all jawed and limbed vertebrates. Studies of phylogeny, species diversity, population structure, conservation, and physiology are accelerated by genomic, transcriptomic and protein sequence data. These data are widely available for many sarcopterygii (coelacanth, lungfish and tetrapods) and actinoptergii (ray-finned fish including teleosts) taxa, but limited for chondrichthyan fishes. In this study, we summarize available data for chondrichthyes and describe resources for one of the largest projects to characterize one of these fish, Leucoraja erinacea, the little skate. SkateBase ( http://skatebase.org) serves as the skate genome project portal linking data, research tools, and teaching resources.
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TL;DR: A thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches, and provided insights on the molecular basis of adaptation to underwater lifestyle and the evolutionary origins of vertebrates.
Abstract: Modern cartilaginous fishes are divided into elasmobranchs (sharks, rays and skates) and chimaeras, and the lack of established whole-genome sequences for the former has prevented our understanding of early vertebrate evolution and the unique phenotypes of elasmobranchs. Here we present de novo whole-genome assemblies of brownbanded bamboo shark and cloudy catshark and an improved assembly of the whale shark genome. These relatively large genomes (3.8–6.7 Gbp) contain sparse distributions of coding genes and regulatory elements and exhibit reduced molecular evolutionary rates. Our thorough genome annotation revealed Hox C genes previously hypothesized to have been lost, as well as distinct gene repertories of opsins and olfactory receptors that would be associated with adaptation to unique underwater niches. We also show the early establishment of the genetic machinery governing mammalian homoeostasis and reproduction at the jawed vertebrate ancestor. This study, supported by genomic, transcriptomic and epigenomic resources, provides a foundation for the comprehensive, molecular exploration of phenotypes unique to sharks and insights into the evolutionary origins of vertebrates. Genomic resources for cartilaginous fishes are scarce. Here, the authors sequence the genome of three sharks and provide insights on the molecular basis of adaptation to underwater lifestyle and the evolutionary origins of vertebrates.
157 citations
TL;DR: It is suggested that at the dawn of the vertebrate lineage, teeth were most likely continuously regenerative structures, and a core set of genes from members of key developmental signalling pathways were instrumental in creating a dental legacy redeployed throughout vertebrate evolution.
87 citations
Cites background or methods from "SkateBase, an elasmobranch genome p..."
...Genome sequencing projects of other members of the chondrichthyan clade will be published soon (Coolen et al., 2008; Wyffels et al., 2014) with representative coverage from both the sharks and rays (elasmobranchs)....
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...Digoxigenin-labeled antisense riboprobes were designed using partial skate (Leucoraja erinacea) and catshark (sometimes referred to as dogfish; Scyliorhynus canicula or Scyliorhinus torazame) EST assemblies (Wyffels et al., 2014) (SkateBase; skatebase....
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..., 2015), increasing availability of genome-scale data (Mulley et al., 2014; Richards et al., 2013; Takechi et al., 2011; Venkatesh et al., 2014; Wyffels et al., 2014) and the wealth of knowledge on conserved genes that regulate tooth development among vertebrate clades (Fraser et al....
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...…were designed using partial skate (Leucoraja erinacea) and catshark (sometimes referred to as dogfish; Scyliorhynus canicula or Scyliorhinus torazame) EST assemblies (Wyffels et al., 2014) (SkateBase; skatebase.org) and the Vertebrate TimeCapsule (VTcap; transcriptome.cdb.riken.go.jp/vtcap)....
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...…al., 2015), increasing availability of genome-scale data (Mulley et al., 2014; Richards et al., 2013; Takechi et al., 2011; Venkatesh et al., 2014; Wyffels et al., 2014) and the wealth of knowledge on conserved genes that regulate tooth development among vertebrate clades (Fraser et al., 2004;…...
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TL;DR: Evidence is provided that the skeletal patterning of the catshark Scyliorhinus canicula pectoral fin is likely driven by a deeply conserved Bmp–Sox9–Wnt Turing network, and that the broad morphological diversity of the distal fin and limb elements arose from the spatial re-organization of a deeply conserve Turing mechanism.
Abstract: A Turing mechanism implemented by BMP, SOX9 and WNT has been proposed to control mouse digit patterning. However, its generality and contribution to the morphological diversity of fins and limbs has not been explored. Here we provide evidence that the skeletal patterning of the catshark Scyliorhinus canicula pectoral fin is likely driven by a deeply conserved Bmp-Sox9-Wnt Turing network. In catshark fins, the distal nodular elements arise from a periodic spot pattern of Sox9 expression, in contrast to the stripe pattern in mouse digit patterning. However, our computer model shows that the Bmp-Sox9-Wnt network with altered spatial modulation can explain the Sox9 expression in catshark fins. Finally, experimental perturbation of Bmp or Wnt signalling in catshark embryos produces skeletal alterations which match in silico predictions. Together, our results suggest that the broad morphological diversity of the distal fin and limb elements arose from the spatial re-organization of a deeply conserved Turing mechanism.
81 citations
TL;DR: It is indicated that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates and transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome.
Abstract: Lungfish and coelacanths are the only living sarcopterygian fish. The phylogenetic relationship of lungfish to the last common ancestor of tetrapods and their close morphological similarity to their fossil ancestors make this species uniquely interesting. However their genome size, the largest among vertebrates, is hampering the generation of a whole genome sequence. To provide a partial solution to the problem, a high-coverage lungfish reference transcriptome was generated and assembled. The present findings indicate that lungfish, not coelacanths, are the closest relatives to land-adapted vertebrates. Whereas protein-coding genes evolve at a very slow rate, possibly reflecting a “living fossil” status, transposable elements appear to be active and show high diversity, suggesting a role for them in the remarkable expansion of the lungfish genome. Analyses of single genes and gene families documented changes connected to the water to land transition and demonstrated the value of the lungfish reference transcriptome for comparative studies of vertebrate evolution.
75 citations
TL;DR: It is shown that the neural substrates of bipedalism are present in the little skate Leucoraja erinacea, whose common ancestor with tetrapods existed ∼420 million years ago, and this indicates that the circuits that are essential for walking evolved through adaptation of a genetic regulatory network shared by all vertebrates with paired appendages.
68 citations
Cites methods from "SkateBase, an elasmobranch genome p..."
...To generate antisense riboprobes for Leucoraja genes, sequence information was obtained from SkateBase (http://skatebase.org) (Wyffels et al., 2014)....
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References
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TL;DR: The goals of the PDB are described, the systems in place for data deposition and access, how to obtain further information and plans for the future development of the resource are described.
Abstract: The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.
34,239 citations
TL;DR: A new membrane protein topology prediction method, TMHMM, based on a hidden Markov model is described and validated, and it is discovered that proteins with N(in)-C(in) topologies are strongly preferred in all examined organisms, except Caenorhabditis elegans, where the large number of 7TM receptors increases the counts for N(out)-C-in topologies.
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TL;DR: The European Molecular Biology Open Software Suite is a mature package of software tools developed for the molecular biology community that includes a comprehensive set of applications for molecular sequence analysis and other tasks and integrates popular third-party software packages under a consistent interface.
9,493 citations
TL;DR: Pfam as discussed by the authors is a widely used database of protein families, containing 14 831 manually curated entries in the current version, version 27.0, and has been updated several times since 2012.
Abstract: Pfam, available via servers in the UK (http://pfam.sanger.ac.uk/) and the USA (http://pfam.janelia.org/), is a widely used database of protein families, containing 14 831 manually curated entries in the current release, version 27.0. Since the last update article 2 years ago, we have generated 1182 new families and maintained sequence coverage of the UniProt Knowledgebase (UniProtKB) at nearly 80%, despite a 50% increase in the size of the underlying sequence database. Since our 2012 article describing Pfam, we have also undertaken a comprehensive review of the features that are provided by Pfam over and above the basic family data. For each feature, we determined the relevance, computational burden, usage statistics and the functionality of the feature in a website context. As a consequence of this review, we have removed some features, enhanced others and developed new ones to meet the changing demands of computational biology. Here, we describe the changes to Pfam content. Notably, we now provide family alignments based on four different representative proteome sequence data sets and a new interactive DNA search interface. We also discuss the mapping between Pfam and known 3D structures.
9,415 citations
TL;DR: SignalP 4.0 was the best signal-peptide predictor for all three organism types but was not in all cases as good as SignalP 3.0 according to cleavage-site sensitivity or signal- peptide correlation when there are no transmembrane proteins present.
Abstract: We benchmarked SignalP 4.0 against SignalP 3.0 and ten other signal peptide prediction algorithms (Fig. 1). We compared prediction performance using the Matthews correlation coefficient16, for which each sequence was counted as a true or false positive or negative. To test SignalP 4.0 performance, we did not use data that had been used in training the networks or selecting the optimal architecture, and the test data did not contain homologs to the training and optimization data (Supplementary Methods). The test set for SignalP 3.0 was also independent of the training set because we removed sequences used to construct SignalP 3.0 and their homologs from the benchmark data. For other algorithms more recent than SignalP 3.0, the benchmark data may include data used to train the methods, possibly leading to slight overestimations of their performance. Our results show that SignalP 4.0 was the best signal-peptide predictor for all three organism types (Fig. 1). This comes at a price, however, because SignalP 4.0 was not in all cases as good as SignalP 3.0 according to cleavage-site sensitivity or signal-peptide correlation when there are no transmembrane proteins present (Supplementary Results). An ideal method would have the best SignalP 4.0: discriminating signal peptides from transmembrane regions
8,370 citations