The cyber-centipede: From Linnaeus to big data

October 28, 2013

The rate of species extinction has lent urgency to the description of new species, but what is the point of new names without meaningful data? A new collaboration between, BGI-Shenzhen, GigaScience and Pensoft Publishers presents an innovative holistic approach to describing new species creating a new kind of 'specimen', the 'cybertype', a 3D computer image that can be downloaded anywhere in the world it is needed and swathe of data types to suit modern biology, including the transcriptome, a DNA barcode, video of the live animal in additional to the traditional morphological description. The approach is illustrated by the description of a new centipede species from Croatia - the 'cyber centipede' Eupolybothrus cavernicolus.

Taxonomic descriptions, introduced by Linnaeus in 1735, are designed to allow scientists to tell one species from another. Now there is a new futuristic method for describing new species that goes far beyond the tradition. The new approach combines several techniques, including next generation molecular methods, barcoding, and novel computing and imaging technologies, that will test the model for big data collection, storage and management in biology. The study has just been published in the Biodiversity Data Journal, with data hosted and curated in BGI's GigaScience GigaDB database.

While 13,095 new animal species were discovered by taxonomists in 2012, animal diversity on the planet continues to decline with unprecedented speed. Concerned with the rapid disappearance rates scientists have been forced towards a so called 'turbo taxonomy' approach, where rapid species description is needed to manage conservation.

While acknowledging the necessity of fast descriptions, the authors of the new study present the other 'extreme' for taxonomic description: "a new species of the future". An international team of scientists from Bulgaria, Croatia, China, UK, Denmark, France, Italy, Greece and Germany illustrated a holistic approach to the description of the new cave dwelling centipede species Eupolybothrus cavernicolus, recently discovered in a remote karst region of Croatia. The project was a collaboration between GigaScience, China National GeneBank, BGI-Shenzhen and Pensoft Publishers.

Eupolybothrus cavernicolus has become the first eukaryotic species for which, in addition to the traditional morphological description, scientists have provided a transcriptomic profile sequenced by BGI, DNA barcoding data, detailed anatomical X-ray microtomography (micro-CT), and a movie of the living specimen to document important traits of its behaviour. By employing micro-CT scanning in a new species, for the first time a high-resolution morphological and anatomical dataset is created, the 'cybertype' giving everyone virtual access to the specimen.

"Communicating the results of next generation sequencing effectively requires the next generation of data publishing" said Prof. Lyubomir Penev, managing director of Pensoft Publishers. "It is not sufficient just to collect 'big' data. The real challenge comes at the point when data should be managed, stored, handled, peer-reviewed, published and distributed in a way that allows for re-use in the coming big data world", concluded Prof. Penev.

Next generation sequencing is moving beyond piecing together a species genetic blueprint to areas such as biodiversity research, with bulk-collected high-throughput "metabarcoding" surveys of species bringing genomics, biomonitoring and species-discovery closer together. This example attempts to integrate data from these different sources, and through curation in the GigaDB database to make it interoperable. "What I find exciting is that you will no longer have to navigate caves or dig through museum collections to view this typed specimen, and multi-dimensional data including its genetic blueprint are freely available to everyone at the touch of a button, allowing you to see this "cyber centipede" alive and in three-dimensions" says Dr Scott Edmunds from BGI and Executive Editor of GigaScience.
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Please find the videos of centipede here:

The cyber-centipede: from Linnaeus to big data http://t.cn/zRaIQNY

Centipede_3D model http://t.cn/zRaVUPD

Original Sources:

Stoev P, Komerički A, Akkari N, Shanlin Liu, Xin Zhou, Weigand AM, Hostens J, Hunter CI, Edmunds SC, Porco D, Zapparoli M, Georgiev T, Mietchen D, Roberts D, Faulwetter S, Smith V, Penev L (2013) 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 1: e1013. DOI: 10.3897/BDJ.1.e1013

Edmunds SC, Hunter CI, Smith V, Stoev P, Penev L (2013) Biodiversity research in the "big data" era: GigaScience and Pensoft work together to publish the most data-rich species description. GigaScience 2:14 doi:10.1186/2047-217X-2-14

Stoev P, Komerički A, Akkari N, Liu S, Zhou X, Weigand AM, Hostens J, Porco D, Penev L (2013): Transcriptomic, DNA barcoding, and micro-CT imaging data from an advanced taxonomic description of a novel centipede species (Eupolybothrus cavernicolus Komerički & Stoev, sp. n.). Gigascience Database. http://dx.doi.org/10.5524/100063

Additional information:

Pensoft and the Natural History Museum London have received financial support by the EU FP7 projects ViBRANT and pro-iBiosphere. The China National GeneBank (CNGB) and GigaScience teams have received support from the BGI. The DNA barcodes were obtained through the International Barcode of Life Project supported by grants from NSERC and from the government of Canada through Genome Canada and the Ontario Genomics Institute.

BGI Shenzhen

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