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      Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data

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          Abstract

          Abstract

          We demonstrate how a classical taxonomic description of a new species can be enhanced by applying new generation molecular methods, and novel computing and imaging technologies. A cave-dwelling centipede, Eupolybothrus cavernicolus Komerički & Stoev sp. n. ( Chilopoda : Lithobiomorpha : Lithobiidae ), found in a remote karst region in Knin, Croatia, is the first eukaryotic species for which, in addition to the traditional morphological description, we provide a fully sequenced transcriptome, a DNA barcode, detailed anatomical X-ray microtomography (micro-CT) scans, and a movie of the living specimen to document important traits of its ex-situ behaviour. By employing micro-CT scanning in a new species for the first time, we create a high-resolution morphological and anatomical dataset that allows virtual reconstructions of the specimen and subsequent interactive manipulation to test the recently introduced ‘cybertype’ notion. In addition, the transcriptome was recorded with a total of 67,785 scaffolds, having an average length of 812 bp and N50 of 1,448 bp (see GigaDB). Subsequent annotation of 22,866 scaffolds was conducted by tracing homologs against current available databases, including Nr, SwissProt and COG. This pilot project illustrates a workflow of producing, storing, publishing and disseminating large data sets associated with a description of a new taxon. All data have been deposited in publicly accessible repositories, such as GigaScience GigaDB, NCBI, BOLD, Morphbank and Morphosource, and the respective open licenses used ensure their accessibility and re-usability.

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          OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

          The concept of orthology provides a foundation for formulating hypotheses on gene and genome evolution, and thus forms the cornerstone of comparative genomics, phylogenomics and metagenomics. We present the update of OrthoDB—the hierarchical catalog of orthologs (http://www.orthodb.org). From its conception, OrthoDB promoted delineation of orthologs at varying resolution by explicitly referring to the hierarchy of species radiations, now also adopted by other resources. The current release provides comprehensive coverage of animals and fungi representing 252 eukaryotic species, and is now extended to prokaryotes with the inclusion of 1115 bacteria. Functional annotations of orthologous groups are provided through mapping to InterPro, GO, OMIM and model organism phenotypes, with cross-references to major resources including UniProt, NCBI and FlyBase. Uniquely, OrthoDB provides computed evolutionary traits of orthologs, such as gene duplicability and loss profiles, divergence rates, sibling groups, and now extended with exon–intron architectures, syntenic orthologs and parent–child trees. The interactive web interface allows navigation along the species phylogenies, complex queries with various identifiers, annotation keywords and phrases, as well as with gene copy-number profiles and sequence homology searches. With the explosive growth of available data, OrthoDB also provides mapping of newly sequenced genomes and transcriptomes to the current orthologous groups.
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            HaMStR: Profile hidden markov model based search for orthologs in ESTs

            Background EST sequencing is a versatile approach for rapidly gathering protein coding sequences. They provide direct access to an organism's gene repertoire bypassing the still error-prone procedure of gene prediction from genomic data. Therefore, ESTs are often the only source for biological sequence data from taxa outside mainstream interest. The widespread use of ESTs in evolutionary studies and particularly in molecular systematics studies is still hindered by the lack of efficient and reliable approaches for automated ortholog predictions in ESTs. Existing methods either depend on a known species tree or cannot cope with redundancy in EST data. Results We present a novel approach (HaMStR) to mine EST data for the presence of orthologs to a curated set of genes. HaMStR combines a profile Hidden Markov Model search and a subsequent BLAST search to extend existing ortholog cluster with sequences from further taxa. We show that the HaMStR results are consistent with those obtained with existing orthology prediction methods that require completely sequenced genomes. A case study on the phylogeny of 35 fungal taxa illustrates that HaMStR is well suited to compile informative data sets for phylogenomic studies from ESTs and protein sequence data. Conclusion HaMStR extends in a standardized manner a pre-defined set of orthologs with ESTs from further taxa. In the same fashion HaMStR can be applied to protein sequence data, and thus provides a comprehensive approach to compile ortholog cluster from any protein coding data. The resulting orthology predictions serve as the data basis for a variety of evolutionary studies. Here, we have demonstrated the application of HaMStR in a molecular systematics study. However, we envision that studies tracing the evolutionary fate of individual genes or functional complexes of genes will greatly benefit from HaMStR orthology predictions as well.
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              Things fall apart: biological species form unconnected parsimony networks.

              The generality of operational species definitions is limited by problematic definitions of between-species divergence. A recent phylogenetic species concept based on a simple objective measure of statistically significant genetic differentiation uses between-species application of statistical parsimony networks that are typically used for population genetic analysis within species. Here we review recent phylogeographic studies and reanalyse several mtDNA barcoding studies using this method. We found that (i) alignments of DNA sequences typically fall apart into a separate subnetwork for each Linnean species (but with a higher rate of true positives for mtDNA data) and (ii) DNA sequences from single species typically stick together in a single haplotype network. Departures from these patterns are usually consistent with hybridization or cryptic species diversity.
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                Author and article information

                Contributors
                URI : urn:lsid:zoobank.org:author:333ECF33-329C-4BC2-BD6A-8D98F6E340D4
                URI : urn:lsid:zoobank.org:author:65524F03-93E0-4782-AB01-2BD3BD0CEE0D
                URI : urn:lsid:zoobank.org:author:8DF67798-8E47-4286-8A79-C3A66B46A10F
                URI : urn:lsid:zoobank.org:author:6D5D96B1-EAD7-4A14-BA52-F919BBC71AA3
                URI : urn:lsid:zoobank.org:author:55AFE973-8749-4C26-A71C-0D2B0E350113
                URI : urn:lsid:zoobank.org:author:C15902F9-515F-4D53-94A7-59058492A569
                URI : urn:lsid:zoobank.org:author:D11BA291-C5CE-472D-BD72-A5469FA61463
                URI : urn:lsid:zoobank.org:author:F4D18C5B-E03E-4B4C-8071-5817E314E2A3
                URI : urn:lsid:zoobank.org:author:F96BF80A-B907-4520-955F-C2F67E238B5D
                URI : urn:lsid:zoobank.org:author:BD56072E-EA94-4F67-A26C-CC53BA478363
                URI : urn:lsid:zoobank.org:author:30E6BE85-C1DA-4215-A07D-652C9770AEC9
                URI : urn:lsid:zoobank.org:author:9D70AF99-0129-4669-86B9-1AA38B1CE555
                URI : urn:lsid:zoobank.org:author:D395CE1E-37C9-4F1E-92A9-9A581C194219
                URI : urn:lsid:zoobank.org:author:7B4DFCC7-57A5-44AF-91F3-422E9A16B36E
                URI : urn:lsid:zoobank.org:author:9BF02566-AF30-47EB-840E-DFC841B6FF84
                URI : urn:lsid:zoobank.org:author:4F2A7E65-9AB8-4CA9-AAF4-6C90DA64E27B
                URI : urn:lsid:zoobank.org:author:1DC4B249-A873-4ACF-AA8F-5FF3AE56803A
                Journal
                Biodivers Data J
                Biodivers Data J
                Biodiversity Data Journal
                Biodiversity Data Journal
                Biodiversity Data Journal
                Pensoft Publishers
                1314-2836
                1314-2828
                2013
                28 October 2013
                : 1
                : e1013
                Affiliations
                []National Museum of Natural History, Sofia, Bulgaria
                []Pensoft Publishers, Sofia, Bulgaria
                [§ ]Croatian Biospeleological Society, Zagreb, Croatia
                [| ]Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
                []China National GeneBank, BGI-Shenzhen, Shenzhen, China
                [# ]Goethe-University, Institute for Ecology, Evolution and Diversity, Frankfurt am Main, Germany
                [†† ]Bruker microCT, Kontich, Belgium
                [‡‡ ]GigaScience, BGI HK Ltd., Tai Po, Hong Kong, China
                [§§ ]Université de Rouen - Laboratoire ECODIV, Mont Saint Aignan Cedex, France
                [|| ]Università degli Studi della Tuscia, Department for Innovation in Biological, Agro-food and Forest systems (DIBAF), Viterbo, Italy
                [¶¶ ]Museum für Naturkunde – Leibniz-Institut für Evolutions- und Biodiversitätsforschung, Berlin, Germany
                [## ]The Natural History Museum, London, United Kingdom
                [††† ]National and Kapodestrian University of Athens, Athens, Greece
                [‡‡‡ ]Hellenic Centre for Marine Research, Heraklion, Greece
                [§§§ ]Institute of Biodiversity & Ecosystem Research - Bulgarian Academy of Sciences and Pensoft Publishers, Sofia, Bulgaria
                Author notes
                Corresponding author: Pavel Stoev ( projects@ 123456pensoft.net ).

                Academic editor: Robert Mesibov.

                Article
                Biodiversity Data Journal 2295
                10.3897/BDJ.1.e1013
                3964625
                24723752
                b82a25e1-9be1-43d4-8439-73b9b15d3a00
                Pavel Stoev, Ana Komerički, Nesrine Akkari, Shanlin Liu, Xin Zhou, Alexander M. Weigand, Jeroen Hostens, Christopher I. Hunter, Scott C. Edmunds, David Porco, Marzio Zapparoli, Teodor Georgiev, Daniel Mietchen, David Roberts, Sarah Faulwetter, Vincent Smith, Lyubomir Penev

                This is an open access article distributed under the terms of the Creative Commons Attribution License 3.0 (CC-BY), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

                History
                : 19 October 2013
                : 23 October 2013
                Page count
                Figures: 22, Tables: 3, References: 68
                Funding
                Funded by: EC FP7 project ViBRANT (Virtual Biodiversity Research and Access Network for Taxonomy, www.vbrant.eu, Contract no. RI-261532) EC FP7 project pro-iBiosphere (Coordination & policy development in preparation for a European Open Biodiversity Knowledge Management System, addressing Acquisition, Curation, Synthesis, Interoperability & Dissemination, http://www.pro-ibiosphere.eu) EC FP 6 Integrated Infrastructure Program SYNTHESYS (DK-TAF)
                Categories
                Lithobiidae
                Molecular Biology
                Taxonomy
                Bioinformatics
                Data Management
                Croatia

                cybertaxonomy,gene sequence data,micro-ct,data integration,molecular systematics,caves,croatia,biospeleology

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