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

  • 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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Metadaten
Author:Pavel Stoev, Ana Komerički, Nesrine Akkari, Shanlin Liu, Xin Zhou, Alexander WeigandORCiDGND, Jeroen Hostens, Christopher I. Hunter, Scott C. Edmunds, David Porco, Marzio Zapparoli, Teodor Georgiev, Daniel Mietchen, David Roberts, Sarah Faulwetter, Vincent Smith, Lyubomir Penev
URN:urn:nbn:de:hebis:30:3-438921
DOI:https://doi.org/10.3897/BDJ.1.e1013
ISSN:1314-2828
Parent Title (German):Biodiversity Data Journal
Publisher:Pensoft Publishers
Place of publication:Sofia
Document Type:Article
Language:English
Year of Completion:2013
Date of first Publication:2013/10/28
Publishing Institution:Universitätsbibliothek Johann Christian Senckenberg
Release Date:2017/10/19
Tag:Croatia; Cybertaxonomy; biospeleology; caves; data integration; gene sequence data; micro-CT; molecular systematics
Volume:1
Issue:e1013
Page Number:37
Note:
© Stoev P et al.. 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.
HeBIS-PPN:42780896
Institutes:Biowissenschaften / Biowissenschaften
Biowissenschaften / Institut für Ökologie, Evolution und Diversität
Dewey Decimal Classification:5 Naturwissenschaften und Mathematik / 57 Biowissenschaften; Biologie / 570 Biowissenschaften; Biologie
Sammlungen:Universitätspublikationen
Sammlung Biologie / Sondersammelgebiets-Volltexte
Licence (German):License LogoCreative Commons - Namensnennung 3.0