StrainInfo introduces electronic passports for microorganisms

Verslyppe, Bert; Smet, Wim De; Baets, Bernard De; Vos, Paul De; Dawyndt, Peter

doi:10.1016/j.syapm.2013.11.002

Cited by 36 publications

(30 citation statements)

References 17 publications

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“…GPI’s goal is to digitize and provide access to type specimens of plants, fungi and algae through community-contributed JSTOR Global Plants online database (http://plants.jstor.org). Other resources include Straininfo, which databases information related to cultures and strains (61). …”

Section: Discussionmentioning

confidence: 99%

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Schoch¹,

Robbertse²,

Robert³

et al. 2014

Database

300

218

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DNA phylogenetic comparisons have shown that morphology-based species recognition often underestimates fungal diversity. Therefore, the need for accurate DNA sequence data, tied to both correct taxonomic names and clearly annotated specimen data, has never been greater. Furthermore, the growing number of molecular ecology and microbiome projects using high-throughput sequencing require fast and effective methods for en masse species assignments. In this article, we focus on selecting and re-annotating a set of marker reference sequences that represent each currently accepted order of Fungi. The particular focus is on sequences from the internal transcribed spacer region in the nuclear ribosomal cistron, derived from type specimens and/or ex-type cultures. Re-annotated and verified sequences were deposited in a curated public database at the National Center for Biotechnology Information (NCBI), namely the RefSeq Targeted Loci (RTL) database, and will be visible during routine sequence similarity searches with NR_prefixed accession numbers. A set of standards and protocols is proposed to improve the data quality of new sequences, and we suggest how type and other reference sequences can be used to improve identification of Fungi.Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353

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Section: Discussionmentioning

confidence: 99%

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Schoch¹,

Robbertse²,

Robert³

et al. 2014

Database

300

218

View full text Add to dashboard Cite

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“…One is through the regular addition of a new Sequencing Project, where a new Organism has to be entered (if not already available in the system). The second is a mass import of cultured organisms from StrainInfo (30) most of which are not yet associated with a Sequencing Project. These organisms are readily available for researchers to choose from while creating a new Sequencing Project in GOLD.…”

Section: Gold Overview and Current Statusmentioning

confidence: 99%

“…Currently, there are 239 100 Organisms in GOLD from which 76 759 are associated with 81 289 Sequencing Projects. Using the strain mapping information provided from StrainInfo (30), equivalent strains from different culture collections are mapped to a single Organism in GOLD.…”

Section: Gold Overview and Current Statusmentioning

confidence: 99%

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

et al. 2016

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The Genomes Online Database (GOLD) (https://gold.jgi.doe.gov) is a manually curated data management system that catalogs sequencing projects with associated metadata from around the world. In the current version of GOLD (v.6), all projects are organized based on a four level classification system in the form of a Study, Organism (for isolates) or Biosample (for environmental samples), Sequencing Project and Analysis Project. Currently, GOLD provides information for 26 117 Studies, 239 100 Organisms, 15 887 Biosamples, 97 212 Sequencing Projects and 78 579 Analysis Projects. These are integrated with over 312 metadata fields from which 58 are controlled vocabularies with 2067 terms. The web interface facilitates submission of a diverse range of Sequencing Projects (such as isolate genome, single-cell genome, metagenome, metatranscriptome) and complex Analysis Projects (such as genome from metagenome, or combined assembly from multiple Sequencing Projects). GOLD provides a seamless interface with the Integrated Microbial Genomes (IMG) system and supports and promotes the Genomic Standards Consortium (GSC) Minimum Information standards. This paper describes the data updates and additional features added during the last two years.

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“…A Xanthomonas albilineans, agente causador da escaldadura das folhas, é uma bactéria gram-negativa da família Xanthomonadaceae, pertencente à ordem Xanthomonadales da subdivisão gama do filo Proteobacteria (Figura 6)._ [25][26] Morfologicamente, a X. albilineans apresenta o formato de bastão alongado, uniflagelada, não esporulante, aeróbica, crescimento lento, aspecto amarelado e colônias não mucoidais.…”

Section: Xanthomonas Albilineansunclassified

“…O cluster de genes XALB1 possui uma sequência que codifica uma proteína similar às que conferem resistência à quinolonas, denominada albG, que possui uma região pentapeptídica responsável por mimetizar a molécula de DNA e impedir a interação da albicidina com a subunidade A da DNA girase. [17][18]25 Em contraste com o observado em outros organismos que produzem moléculas inibidoras de DNA girase, não existe evidências de subunidades A ou B resistentes a albicidinas em X. albilineans. A regulação de biossíntese de albicidinas, embora não relacionada ao crescimento bacteriano, é feita baseada na abundância de nutrientes no meio, principalmente aminoácidos e fontes de fósforo e nitrogênio.…”

Section: A Albicidinaunclassified

Estudos estruturais de enzimas da via de biossíntese de folatos de <i>Xanthomonas albilineans</i> para o desenvolvimento de novos candidatos a agroquímicos para a cultura de cana-de-açúcar

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StrainInfo introduces electronic passports for microorganisms

Cited by 36 publications

References 17 publications

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Finding needles in haystacks: linking scientific names, reference specimens and molecular data for Fungi

Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements

Estudos estruturais de enzimas da via de biossíntese de folatos de <i>Xanthomonas albilineans</i> para o desenvolvimento de novos candidatos a agroquímicos para a cultura de cana-de-açúcar

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