論文 - 詳細
| RRC ID | 29280 |
|---|---|
| 著者 | Yarza P, Spröer C, Swiderski J, Mrotzek N, Spring S, Tindall BJ, Gronow S, Pukall R, Klenk HP, Lang E, Verbarg S, Crouch A, Lilburn T, Beck B, Unosson C, Cardew S, Moore ER, Gomila M, Nakagawa Y, Janssens D, De Vos P, Peiren J, Suttels T, Clermont D, Bizet C, Sakamoto M, Iida T, Kudo T, Kosako Y, Oshida Y, Ohkuma M, R Arahal D, Spieck E, Pommerening Roeser A, Figge M, Park D, Buchanan P, Cifuentes A, Munoz R, Euzéby JP, Schleifer KH, Ludwig W, Amann R, Glöckner FO, Rosselló-Móra R. |
| タイトル | Sequencing orphan species initiative (SOS): Filling the gaps in the 16S rRNA gene sequence database for all species with validly published names. |
| ジャーナル | Syst Appl Microbiol |
| Abstract |
High 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, are a prerequisite for their accurate affiliations within the global genealogical classification and for the recognition of potential new taxa. During the last few years, the Living Tree Project (LTP) has taken care to create a high quality, aligned 16S and 23S rRNA gene sequence database of all type strains. However, the manual curation of the sequence dataset and type strain information revealed that a total of 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 an 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 has coordinated a network of researchers and culture collections in order to improve the situation by (re)-sequencing the type strains of these "orphan" species. As a result, we can now report 351 16S rRNA gene sequences of type strains. Nevertheless, 201 species could not be sequenced because cultivable type strains were not available (121), the cultures had either been lost or were never deposited in the first place (66), or it was not possible 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 in order to help solve some of these issues. |
| 巻・号 | 36(1) |
| ページ | 69-73 |
| 公開日 | 2013-2-1 |
| DOI | 10.1016/j.syapm.2012.12.006 |
| PII | S0723-2020(13)00004-0 |
| PMID | 23410935 |
| MeSH | Bacteria / classification* Bacteria / genetics* Classification / methods DNA, Bacterial / chemistry DNA, Bacterial / genetics* DNA, Ribosomal / chemistry DNA, Ribosomal / genetics Phylogeny* RNA, Ribosomal, 16S / genetics* Sequence Analysis, DNA* |
| IF | 3.224 |
| 引用数 | 45 |
| WOS 分野 | BIOTECHNOLOGY & APPLIED MICROBIOLOGY MICROBIOLOGY |
| オルトメトリクス指標 |
オルトメトリクス指標項目
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| 最多言及媒体 | Wikipedia |
| 各媒体での言及数の合計 | 8 |
| 過去6か月間でのオルトメトリクス指標の変動値 | 0.0 |
| リソース情報 | |
| 一般微生物 | JCM 1392 JCM 1395 JCM 1400 JCM 3136 JCM 3315 JCM 3367 JCM 3724 JCM 6889 JCM 9188 JCM 9533 JCM 9537 JCM 10083 JCM 11021 JCM 11220 JCM 11496 JCM 11608 JCM 12952 JCM 13392 JCM 13574 JCM 13874 JCM 14655 JCM 15662 JCM 16132 |