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: Lit...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Pensoft Publishers
2016-10-01
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| Series: | Biodiversity Data Journal |
| Subjects: | |
| Online Access: | http://bdj.pensoft.net/articles.php?id=1013 |
| _version_ | 1811312958961090560 |
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| author | Pavel Stoev Ana Komerički Nesrine Akkari Shanlin Liu Xin Zhou Alexander Weigand Jeroen Hostens Christopher Hunter Scott Edmunds David Porco Marzio Zapparoli Teodor Georgiev Daniel Mietchen David Roberts Sarah Faulwetter Vincent Smith Lyubomir Penev |
| author_facet | Pavel Stoev Ana Komerički Nesrine Akkari Shanlin Liu Xin Zhou Alexander Weigand Jeroen Hostens Christopher Hunter Scott Edmunds David Porco Marzio Zapparoli Teodor Georgiev Daniel Mietchen David Roberts Sarah Faulwetter Vincent Smith Lyubomir Penev |
| author_sort | Pavel Stoev |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-04-13T10:47:04Z |
| format | Article |
| id | doaj.art-7e7d194134e545b8860f41d9555ad7ab |
| institution | Directory Open Access Journal |
| issn | 1314-2836 1314-2828 |
| language | English |
| last_indexed | 2024-04-13T10:47:04Z |
| publishDate | 2016-10-01 |
| publisher | Pensoft Publishers |
| record_format | Article |
| series | Biodiversity Data Journal |
| spelling | doaj.art-7e7d194134e545b8860f41d9555ad7ab2022-12-22T02:49:47ZengPensoft PublishersBiodiversity Data Journal1314-28361314-28282016-10-01113710.3897/BDJ.1.e10131013Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging dataPavel Stoev0Ana Komerički1Nesrine Akkari2Shanlin Liu3Xin Zhou4Alexander Weigand5Jeroen Hostens6Christopher Hunter7Scott Edmunds8David Porco9Marzio Zapparoli10Teodor Georgiev11Daniel Mietchen12David Roberts13Sarah Faulwetter14Vincent Smith15Lyubomir Penev16National Museum of Natural HistoryCroatian Biospeleological SocietyNatural History Museum of Denmark, University of CopenhagenChina National GeneBank, BGI-ShenzhenChina National GeneBank, BGI-ShenzhenGoethe-University, Institute for Ecology, Evolution and DiversityBruker microCTGigaScience, BGI HK Ltd., Tai PoGigaScience, BGI HK Ltd., Tai PoUniversité de Rouen - Laboratoire ECODIVUniversità degli Studi della Tuscia, Department for Innovation in Biological, Agro-food and Forest systems (DIBAF)Pensoft PublishersMuseum für Naturkunde – Leibniz-Institut für Evolutions- und BiodiversitätsforschungThe Natural History MuseumNational and Kapodestrian University of AthensThe Natural History MuseumInstitute of Biodiversity & Ecosystem Research - Bulgarian Academy of Sciences and Pensoft PublishersWe 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.http://bdj.pensoft.net/articles.php?id=1013Cybertaxonomygene sequence datamicro-CTdata integrationmolecular systematicscaves |
| spellingShingle | Pavel Stoev Ana Komerički Nesrine Akkari Shanlin Liu Xin Zhou Alexander Weigand Jeroen Hostens Christopher Hunter Scott Edmunds David Porco Marzio Zapparoli Teodor Georgiev Daniel Mietchen David Roberts Sarah Faulwetter Vincent Smith Lyubomir Penev Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data Biodiversity Data Journal Cybertaxonomy gene sequence data micro-CT data integration molecular systematics caves |
| title | Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data |
| title_full | Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data |
| title_fullStr | Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data |
| title_full_unstemmed | Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data |
| title_short | Eupolybothrus cavernicolus Komerički & Stoev sp. n. (Chilopoda: Lithobiomorpha: Lithobiidae): the first eukaryotic species description combining transcriptomic, DNA barcoding and micro-CT imaging data |
| title_sort | eupolybothrus cavernicolus komericki amp amp stoev sp n chilopoda lithobiomorpha lithobiidae the first eukaryotic species description combining transcriptomic dna barcoding and micro ct imaging data |
| topic | Cybertaxonomy gene sequence data micro-CT data integration molecular systematics caves |
| url | http://bdj.pensoft.net/articles.php?id=1013 |
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