Toward the DNA Library of Life

Line Le Gall, Frédéric Delsuc, Stéphane Hourdez, Guillaume Lecointre, Jean-Yves Rasplus

Abstract


The special set of papers entitled “DNA Library of Life” constitutes an outcome of the project “Bibliothèque du vivant” (BdV), which aims to promote the molecular taxonomy of eukaryotes by offering research teams the possibility to produce and manage a molecular library linked with specimens deposited in natural history museums. The project was funded by three French institutions (the CNRS, INRA and MNHN), and provided access to the sequencing power offered by the Genoscope for 105 teams between 2011 and 2013. It was subsequently supported by the CNRS through the “Groupement de Recherche Génomique Environnementale”. The scientific objectives of this programme were threefold: 1) species delimitation among species complexes; 2) phylogenetic reconstruction (including phylogenomics); and 3) metabarcoding and improving NGS methods for systematic purposes. Within the present collection, 19 papers contribute to these objectives across a large taxonomic range and a worldwide geographic coverage. These papers propose taxonomic novelties (22 new species and 3 new genera) in both animal and plant taxa.

Keywords


Census of Life; eukaryotic biodiversity; molecular assisted systematics; Museum life; species description

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DOI: https://doi.org/10.5852/ejt.2017.266

References


Anonymous. 2017. National Center for Biotechnology – Taxonomy. NCBI, Bethesda, MD, USA. Available from https://www.ncbi.nlm.nih.gov/taxonomy [accessed 7 Jan. 2017].

Appeltans W., Ahyong S.T., Anderson G., Angel M.V., Artois T., Bailly N., Bamber R., Barber A., Bartsch I., Berta A., Błażewicz-Paszkowycz M., Bock P., Boxshall G., Boyko C.B., Brandão S.N., Bray R.A., Bruce N.L., Cairns S.D., Chan T.-Y., Cheng L., Collins A.G., Cribb T., Curini-Galletti M., Dahdouh-Guebas F., Davie P.J.F., Dawson M.N., De Clerck O., Decock W., De Grave S., de Voogd N.J., Domning D.P., Emig C.C., Erséus C., Eschmeyer W., Fauchald K., Fautin D.G., Feist S.W., Fransen C.H.J.M., Furuya H., Garcia-Alvarez O., Gerken S., Gibson D., Gittenberger A., Gofas S., Gómez-Daglio L., Gordon D.P., Guiry M.D., Hernandez F., Hoeksema B.W., Hopcroft R.R., Jaume D., Kirk P., Koedam N., Koenemann S., Kolb J.B., Kristensen R.M., Kroh A., Lambert G., Lazarus D.B., Lemaitre R., Longshaw M., Lowry J., Macpherson E., Madin L.P., Mah C., Mapstone G., McLaughlin P.A., Mees J., Meland K., Messing C.G., Mills C.E., Molodtsova T.N., Mooi R., Neuhaus B., Ng P.K.L., Nielsen C., Norenburg J., Opresko D.M., Osawa M., Paulay G., Perrin W., Pilger J.F., Poore G.C.B., Pugh P., Read G.B., Reimer J.D., Rius M., Rocha R.M., Saiz-Salinas J.I., Scarabino V., Schierwater B., Schmidt-Rhaesa A., Schnabel K.E., Schotte M., Schuchert P., Schwabe E., Segers H., Self-Sullivan C., Shenkar N., Siegel V., Sterrer W., Stöhr S., Swalla B., Tasker M.L., Thuesen E.V., Timm T., Todaro M.A., Turon X., Tyler S., Uetz P., van der Land J., Vanhoorne B., van Ofwegen L.P., van Soest R.W.M., Vanaverbeke J., Walker-Smith G., Walter T.C., Warren A., Williams G.C., Wilson S.P., Costello M.J. 2012. The magnitude of global marine species diversity. Current Biology 22: 2189–2202. http://dx.doi.org/10.1016/j.cub.2012.09.036

Azofeifa-Bolaños J.B., Gigant L.R., Nicolás-García M., Pignal M., Tavares-González F.B., Hágsater E., Salazar-Chávez G.A., Reyes-López D., Archila-Morales F.L., García-García J.A., da Silva D., Allibert A., Solano-Campos F., Rodríguez-Jimenes G.d.C., Paniagua-Vásquez A., Besse P., Pérez-Silva A. & Grisoni M. In press. A new vanilla species from Costa Rica closely related to V. planifolia (Orchidaceae).European Journal of Taxonomy.

Blaxter M.L. 2004. The promise of a DNA taxonomy. Philosophical Transactions of the Royal Society 359: 669–679. http://dx.doi.org/10.1098/rstb.2003.1447

Castelin M., de Mazancourt V., Marquet G., Zimmerman G. & Keith P. In press a. Genetic and morphological evidence for cryptic species in Macrobrachium australe and resurrection of M. ustulatum (Crustacea, Palaemonidae). European Journal of Taxonomy.

Castelin M., Williams S., Buge B., Maestrati P., Lambourdière J., Ozawa T., Utge J., Couloux A., Alf A. & Samadi S. In press b. Untangling species identity in gastropods with polymorphic shells in the genus Bolma (Mollusca, Vetigastropoda). European Journal of Taxonomy.

Coissac E., Hollingsworth P.M., Lavergne S. & Taberlet P. 2016. From barcodes to genomes: extending the concept of DNA barcoding. Molecular Ecology 25: 1423–1428. http://dx.doi.org/10.1111/mec.13549

Collins R.A. & Cruickshank R.H. 2012. The seven deadly sins of DNA barcoding. Molecular Ecology Resources 13 (6): 969–975. http://dx.doi.org/10.1111/1755-0998.12046

Costello M.J., May R.M. & Stork N.E. 2013. Can we name Earth’s species before they go extinct? Science 339: 413–416.

Fedosov A.E., Stahlschmidt P., Puillandre N., Aznar-Cormano L. & Bouchet P. In press. Not all spotted cats are leopards: evidence for a Hemilienardia ocellata species complex (Gastropoda: Conoidea: Raphitomidae). European Journal of Taxonomy.

Fontaine B., Perrard A. & Bouchet P. 2012. 21 years of shelf life between discovery and description of new species. Current Biology 22: R943–R944.

Galindo L.A., Kool H.H. & Dekker H. In press. Review of the Nassarius pauperus (Gould, 1850) complex (Nassariidae). Part 3, reinstatement of the genus Reticunassa with the description of six new species. European Journal of Taxonomy.

Galkowski C., Lebas C., Wegnez P., Lenoir A. & Blatrix R. In press. Re-description of Proformica nasuta (Nylander, 1856) (Hymenoptera, Formicidae) using an integrative approach. European Journal of Taxonomy.

Hamarneh S. 1960. Measuring the Invisible World. The life and works of Antoni van Leeuwenhoek (book review). Science 132: 289–290. http://dx.doi.org/10.1126/science.132.3422.289

Hawksworth D.L. 2001. The magnitude of fungal diversity: the 1.5 million species estimate revisited. Mycological Research 105: 1422–1432. http://dx.doi.org/10.1017/S0953756201004725

Hebert P.D.N., Cywinska A., Ball S.L. & deWaard J.R. 2003. Biological identifications through DNA barcodes. Proceedings of the Royal Society B 270: 313–321. http://dx.doi.org/10.1098/rspb.2002.2218

ICZN. 1999. International Commission of Zoological Nomenclature. The Code Online. Available from http://www.iczn.org/iczn/index.jsp [accessed 7 Jan. 2017].

Legendre F., Grandcolas P. & Thouzé F. In press. Molecular phylogeny of Blaberidae (Dictyoptera, Blattodea) with implications for taxonomy and evolutionary scenarios. European Journal of Taxonomy.

Le Ru B., Capdevielle-Dulac C., Musyoka B.K., Pallangyo B., Njaku M., Mubenga O., Chipabika G., Ndemah R., Bani G., Molo R. Ong’amo G. & Kergoat G.J. In press. Phylogenetic analysis and systematics of the Acrapex unicolora Hampson species complex (Lepidoptera, Noctuidae, Noctuinae, Apameini), with the description of five new species from the Afrotropics.

Linnaeus C. 1753. Species Plantarum, Exhibentes Plantas Rite Cognitas, ad Genera Relatas, cum Differentiis Specificis, Nominibus Trivialibus, Synonymis Selectis, Locis Natalibus, Secundum Systema Sexuale Digestas. Volume 1. Laurentii Salvii, Holmiae [Stockholm]. Available from http://www.biodiversitylibrary.org/item/13829 [accessed 20 Jan. 2017].

Manghisi A., Le Gall L., Bonillo C., Gargiulo G.M., Ribeira M.A. & Morabito M. In press. An assessment of the taxonomic status of the Mediterranean endemic genus Acrodiscus Zanardini (Halymeniales, Rhodophyta). European Journal of Taxonomy.

Mayr E. 1982. The growth of biological thought: diversity, evolution, and inheritance. Harvard University Press, Cambridge, MA, USA.

McNeill J. & International Association for Plant Taxonomy (eds) 2012. International code of nomenclature for algae, fungi and plants (Melbourne code): adopted by the Eighteenth International Botanical Congress Melbourne, Australia, July 2011. Koeltz Scientific Books, Königstein, Germany. Available from http://www.iapt-taxon.org/nomen/main.php?page=title [accessed 20 Jan. 2017].

Mora C., Tittensor D.P., Adl S., Simpson A.G.B. & Worm B. 2011. How many species are there on Earth and in the ocean? PLoS Biology 9: e1001127. http://dx.doi.org/10.1371/journal.pbio.1001127

Ohler A. & Nicolas V. In press. Which frog’s legs do froggies eat? The use of DNA barcoding for identification of deep frozen frog legs (Dicroglossidae, Amphibia) commercialized in France. European Journal of Taxonomy.

Philippe H., de Vienne D.M., Ranwez V., Roure B., Baurain D. & Delsuc F. In press. Pitfalls in supermatrix phylogenomics. European Journal of Taxonomy.

Pons J., Barraclough T., Gomez-Zurita J., Cardoso A., Duran D., Hazell S., Kamoun S., Sumlin W. & Vogler A. 2006. Sequence-based species delimitation for the DNA taxonomy of undescribed insects. Systematic Biology 55: 595–609. http://dx.doi.org/10.1080/10635150600852011

Pringent S.R., Suwalski A. & Veuille M. In press. Connecting systematic and ecological studies using DNA barcoding in a population survey of Drosophilidae (Diptera) from Mt Oku (Cameroon). European Journal of Taxonomy.

Puillandre N., Lambert A., Brouillet S. & Achaz G. 2012. ABGD, Automatic Barcode Gap Discovery for primary species delimitation. Molecular Ecology 21 (8): 1864–1877. http://dx.doi.org/10.1111/j.1365-294X.2011.05239.x

Quast C., Pruesse E., Yilmaz P., Gerken J., Schweer T., Yarza P., Peplies J. & Glockner F.O. 2013. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Research 41: D590–D596. http://dx.doi.org/10.1093/nar/gks1219

Rabeau L., Gradstein S.R., Dubuisson J.-Y., Nebel M., Quandt D. & Reeb C. In press. New insights into the phylogeny and relationships within the worldwide genus Riccardia (Aneuraceae, Marchantiophytina). European Journal of Taxonomy.

Ramage T., Martins-Simoes P., Mialdea G., Allemand R., Duplouy A., Rousse P., Davies N., Roderick G.K. & Charlat S. In press. A DNA barcode-based survey of terrestrial arthropods in the Society Islands of French Polynesia: host diversity within the SymbioCode Project. European Journal of Taxonomy.

Ratnasingham S. & Hebert P.D.N. 2013. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE 8: e66213. http://dx.doi.org/10.1371/journal.pone.0066213

Régnier C., Achaz G., Lambert A., Cowie R.H., Bouchet P. & Fontaine B. 2015. Mass extinction in poorly known taxa. Proceedings of the National Academy of Sciences 112: 7761–7766. http://dx.doi.org/10.1073/pnas.1502350112

Rousseau F., Gey D., Kurihara A., Maggs C.A., Martin-Lescanne J., Payri C., Reviers B. de, Sherwood A.R. & Le Gall L. In press. Molecular phylogenies support taxonomic revision of three species of Laurencia (Rhodomelaceae, Rhodophyta), with the description of a new genus. European Journal of Taxonomy.

Roux C., Fraisse C., Romiguier J., Anciaux Y., Galtier N. & Bierne N. 2016. Shedding light on the grey zone of speciation along a continuum of genomic divergence. PLoS Biology 14 (12): e2000234. http://dx.doi.org/10.1371/journal.pbio.2000234

Sabroux R., Corbari L., Krapp F., Bonillo C., Le Prieur S. & Hassanin A. In press. Biodiversity and phylogeny of Ammotheidae (Arthropoda: Pycnogonida). European Journal of Taxonomy.

Soldati L., Condamine F.L., Clamens A.-L. & Kergoat G.J. In press. Documenting tenebrionid diversity: progress on Blaps Fabricius (Coleoptera, Tenebrionidae, Tenebrioninae, Blaptini) systematics, with the description of five new species. European Journal of Taxonomy.

Tu V.T., Csorba G., Ruedi M., Furey N.M., Son N.T., Thong V.D., Bonillo C. & Hassanin A. In press. Comparative phylogeography of bamboo bats of the genus Tylonycteris (Chiroptera, Vespertilionidae) in Southeast Asia. European Journal of Taxonomy.

Vargas C. de, Audic S., Henry N., Decelle J., Mahe F., Logares R., Lara E., Berney C., Le Bescot N., Probert I., Carmichael M., Poulain J., Romac S., Colin S., Aury J.-M., Bittner L., Chaffron S., Dunthorn M., Engelen S., Flegontova O., Guidi L., Horak A., Jaillon O., Lima-Mendez G., Luke J., Malviya S., Morard R., Mulot M., Scalco E., Siano R., Vincent F., Zingone A., Dimier C., Picheral M., Searson S., Kandels-Lewis S., Tara Oceans Coordinators, Acinas S.G., Bork P., Bowler C., Gorsky G., Grimsley N., Hingamp P., Iudicone D., Not F., Ogata H., Pesant S., Raes J., Sieracki M.E., Speich S., Stemmann L., Sunagawa S., Weissenbach J., Wincker P., Karsenti E., Boss E., Follows M., Karp-Boss L., Krzic U., Reynaud E.G., Sardet C., Sullivan M.B. & Velayoudon D. 2015. Eukaryotic plankton diversity in the sunlit ocean. Science 348 (6237): e1261605. http://dx.doi.org/10.1126/science.1261605

Veron G., Bonillo C., Hassanin A. & Jennings A.P. In press. Molecular systematics and biogeography of the Hemigalinae civets (Mammalia, Carnivora). European Journal of Taxonomy.

Watson J.D. & Crick F.H.C. 1953. Molecular structure of nucleic acids: A structure for deoxyribose nucleic acid. Nature 171: 737–738. http://dx.doi.org/10.1038/171737a0

Yahr R., Schoch C.L. & Dentinger B.T.M. 2016. Scaling up discovery of hidden diversity in fungi: impacts of barcoding approaches. Philosophical Transactions of the Royal Society B 371: e20150336. http://dx.doi.org/10.1098/rstb.2015.0336

Yang Z. & Rannala B. 2014. Unguided species delimitation using DNA sequence data from multiple loci. Molecular Biology and Evolution 31 (12): 3125–3135. http://dx.doi.org/10.1093/molbev/msu279

Yilmaz P., Parfrey L.W., Yarza P., Gerken J., Pruesse E., Quast C., Schweer T., Peplies J., Ludwig W. & Glöckner F.O. 2014. The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks. Nucleic Acids Research 42: D643–D648. http://dx.doi.org/10.1093/nar/gkt1209

Zhang J., Kapli P., Pavlidis P. & Stamatakis A. 2013. A general species delimitation method with applications to phylogenetic placements. Bioinformatics 29: 2869–2876. http://dx.doi.org/10.1093/bioinformatics/btt499


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