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. 2013 Oct 28:(1):e1013.
doi: 10.3897/BDJ.1.e1013. eCollection 2013.

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

Pavel Stoev  1 , Ana Komerički  2 , Nesrine Akkari  3 , Shanlin Liu  4 , Xin Zhou  4 , Alexander M Weigand  5 , Jeroen Hostens  6 , Christopher I Hunter  7 , Scott C Edmunds  7 , David Porco  8 , Marzio Zapparoli  9 , Teodor Georgiev  10 , Daniel Mietchen  11 , David Roberts  12 , Sarah Faulwetter  13 , Vincent Smith  12 , Lyubomir Penev  14
Affiliations

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

Pavel Stoev et al. Biodivers Data J. .

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.

Keywords: Croatia; Cybertaxonomy; biospeleology; caves; data integration; gene sequence data; micro-CT; molecular systematics.

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Figures

Figure 1.
Figure 1.
Habitus of Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype, ex situ.
Figure 2a.
Figure 2a.
cephalic plate, dorsal view
Figure 2b.
Figure 2b.
ocelli and Tömösváry’s organ. Abbreviations: ocellus (O) and Tömösváry’s organ (T)
Figure 3a.
Figure 3a.
clypeus, ventral view; most setae broken off
Figure 3b.
Figure 3b.
tip of antenna
Figure 4a.
Figure 4a.
forcipules, ventral view
Figure 4b.
Figure 4b.
close up of coxosternum, ventral view. Abbreviations: porodonts (po).
Figure 5a.
Figure 5a.
tergite 7, dorsal view
Figure 5b.
Figure 5b.
tergites 12-13, dorsal view
Figure 6a.
Figure 6a.
tergite 14 and intermediate tergite, posteriodorsal view. Abbreviations: seta-free areas (sfa).
Figure 6b.
Figure 6b.
pretarsus of leg 10, ventral view. Abbreviations: anterior accessory claw (a), posterior accessory claw (p).
Figure 7a.
Figure 7a.
tarsus 1, tarsus 2 and pretarsus of leg 10, lateral view. Abbreviations: pectinal setae (ps).
Figure 7b.
Figure 7b.
pretarsus of leg 15
Figure 8a.
Figure 8a.
prefemur 15, mesoventral view. Abbreviations: prefemoral knob (pk), circular setose protuberance (cp), cluster of setae (sc).
Figure 8b.
Figure 8b.
close up of the prefemoral knob, ventral view
Figure 9a.
Figure 9a.
close up of the clusp of setae on male prefemur 15
Figure 9b.
Figure 9b.
close up of the setose protuberance on male prefemur 15
Figure 10a.
Figure 10a.
close up of the tip of prefemoral spine p
Figure 10b.
Figure 10b.
coxal pore pit, meso-ventral view
Figure 11.
Figure 11.
Eupolybothrus cavernicolus Komerički & Stoev sp. n., male paratype. Genitalia, posterio-dorsal view.
Figure 12.
Figure 12.
Map of Croatia showing the locality of Eupolybothrus cavernicolus Komerički & Stoev sp. n.
Figure 13.
Figure 13.
Entrance of cave Miljacka II, type locality of Eupolybothrus cavernicolus Komerički & Stoev sp. n.
Figure 14a.
Figure 14a.
ocelli
Figure 14b.
Figure 14b.
forcipules, ventral view
Figure 15a.
Figure 15a.
tergite 14 and intermediate tergite, dorsal view
Figure 15b.
Figure 15b.
close up of posterior part of prefemur of leg 14 showing the expanded distal part bearing feebly defined setose protuberance
Figure 16.
Figure 16.
Eupolybothrus leostygis (Verhoeff, 1899), male: prefemur 15 showing the bare knob, dorsal view.
Figure 17a.
Figure 17a.
Eupolybothrus tabularum
Figure 17b.
Figure 17b.
Eupolybothrus excellens
Figure 18a.
Figure 18a.
Eupolybothrus caesar
Figure 18b.
Figure 18b.
Eupolybothrus spiniger
Figure 19.
Figure 19.
Delineation of Eupolybothrus species – Neighbor joining tree K2P distances. Visualised are the clusters obtained from the reversed Statistical Parsimony (SP) method and the Automatic Barcoding Gap Discovery (ABGD) procedure. Bootstrap support for the identified lineages are given above. The intraspecific genetic variability is given for each cluster. Source data is available in Suppl. material 1.
Figure 20a.
Figure 20a.
E-value, identity and species distribution statistics of the sequences that can find homologs on Nr database
Figure 20b.
Figure 20b.
COG functional classification of the transcripts
Figure 20c.
Figure 20c.
GO categories of the transcripts
See this image and copyright information in PMC

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