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Sequencing Orphan Species initiative (SOS): filling the gaps in the 16S rRNA gene sequence database for all species with validly published names

AuthorsYarza, Pablo ; Muñoz, Raúl; Schleifer, Karl-Heinz; Ludwig, Wolfgang; Amann, Rudolf; Glöckner, Frank Oliver; Rosselló-Mora, Ramón
Issue Date10-Mar-2013
CitationJahrestagung der VAAM 2013 = Annual Conference 2013 of the Association for General and Applied Microbiology (VAAM)
AbstractHigh quality 16S ribosomal RNA (rRNA) gene sequences from the type strains of all species with validly published names as defined by the International Code of Nomenclature of Bacteria is a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potentially new species. During the last few years the Living Tree Project (LTP, http://www.arb-silva.de/projects/living-tree) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. The manual curation of the sequence dataset and type strain information revealed that in total 552 “orphan” species (about 5.7% of the currently classified species) had to be excluded from the reference trees. Among them, 322 type strains were not represented by a SSU entry in the public sequence repositories. The remaining 230 type strains had to be discarded due to bad sequence quality. Since 2010, the LTP team coordinated a network of researchers and culture collections to improve the situation by (re)-sequencing the type strains of these “orphan” species. Here we report 351 16S rRNA gene sequences of type strains. 201 species could not be sequenced because either cultivable type strains were not available (121), or the cultures had either been lost or were never deposited in first place (66), or due to other constraints (14). The International Code of Nomenclature of Bacteria provides a number of mechanisms to deal with the problem of missing type strains and we recommend that due consideration be given to the appropriate mechanisms to help solve some of these issues
DescriptionPóster presentado en la Annual Conference 2013 of the Association for General and Applied Microbiology (VAAM) in collaboration with the Royal Netherlands Socity for Microbiology (KNVM), celebrada del 10 al 13 de marzo de 2013 en Bremen (Alemania)
Appears in Collections:(IMEDEA) Comunicaciones congresos
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