Petabyte-scale innovations at the European Nucleotide Archive

Cochrane, Guy; Akhtar, Ruth; Bonfield, James K.; Bower, Lawrence; Demiralp, Fehmi; Faruque, Nadeem; Gibson, Richard L.; Hoad, Gemma; Hubbard, Tim; Hunter, Chris; Jang, Mikyung; Juhos, Szilveszter; Leinonen, Rasko; Leonard, Steven; Lin, Quan; López, Rodrigo; Lorenc, Dariusz; McWilliam, Hamish; Mukherjee, Gaurab; Plaister, Sheila; Radhakrishnan, Rajesh; Robinson, Stephen J.; Sobhany, Siamak; Hoopen, Petra ten; Vaughan, R. W.; Zalunin, Vadim; Birney, Ewan

doi:10.1093/nar/gkn765

Cited by 83 publications

(47 citation statements)

References 13 publications

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“…The DNA sequences of the partial 16S rRNA genes of 12 isolates (between 804 and 1,492 bp in sizes) were deposited in the EMBL Nucleotide Sequence Database (Cochrane et al 2009) under accession numbers FN394501 to FN394512.…”

Section: Nucleotide Sequence Accession Numbersmentioning

confidence: 99%

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

et al. 2009

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Purpose The role of dominant bacterial groups in the plant rhizosphere, e.g., those belonging to the phyla Acidobacteria and Verrucomicrobia, has, so far, not been elucidated, and this is mainly due to the lack of culturable representatives. This study aimed to isolate hithertouncultured bacteria from the potato rhizosphere by a combination of cultivation approaches. Materials and methods An agar medium low in carbon availability (oligotrophic agar medium) and either amended with potato root exudates or catalase or left unamended was used with the aim to improve the culturability of bacteria from the potato rhizosphere. The colony forming unit numbers based on colonies and microcolonies were compared with microscopically determined fluorescence-stained cell numbers. Taxonomical diversity of the colonies was compared with that of library clones made from rhizosphere DNA, on the basis of 16S rRNA gene comparisons.Results and discussion The oligotrophic media amended or not with catalase or rhizosphere extract recovered up to 33.6% of the total bacterial numbers, at least seven times more than the recovery observed on R2A. Four hithertouncultured Verrucomicrobia subdivision 1 representatives were recovered on agar, but representatives of this group were not found in the clone library. Conclusions The use of oligotrophic medium and its modifications enabled the growth of colony numbers, exceeding those on classical agar media. Also, it led to the isolation of hitherto-uncultured bacteria from the potato rhizosphere. Further improvement in cultivation will certainly result in the recovery of other as-yet-unexplored bacteria from the rhizosphere, making these groups accessible for further investigation, e.g., with respect to their possible interactions with plants.

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Section: Nucleotide Sequence Accession Numbersmentioning

confidence: 99%

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

et al. 2009

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“…Sequences were analyzed with the Staden Package version 16.0 (Staden 1999; http://staden.sourceforge.net/), and sequence alignments were performed in BioEdit version 7.0.9 (Hall 1999) using ClustalW multiple alignment (Thompson et al 1994). FASTA searches of sequences were done against the EMBL (Cochrane et al 2008) and NCBI databases (Baker et al 2000).…”

Section: Methodsmentioning

confidence: 99%

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

2016

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Abstract:The development of sequence characterized amplified region (SCAR) markers derived from amplified fragment length polymorphisms (AFLPs) is described for Shorea leprosula. An AFLP fragment that showed nearly complete differentiation between Borneo and Sumatra was gel-extracted, sequenced, and converted into a SCAR marker using the inverse polymerase chain reaction (PCR) technique. The single nucleotide polymorphism (SNP) that originally caused the AFLP was found in the MseI restriction site. Differentiation between islands was detected either as size variation of the codominant SCAR marker or after digestion of the PCR products with the restriction enzyme MseI (PCR-RFLP). Size variation was due to insertions/deletions found within the sequenced region that flanked the original AFLP fragment. After genotyping 151 samples of S. leprosula from 14 populations in Sumatra and Borneo, all but one sample from Sumatra were homozygous for one size variant (427 bp), while S. leprosula populations from Borneo showed different genotypes than Sumatra populations and variation not only among populations but also within populations. Complete differentiation and fixation on alternative variants was found for the geographic regions of Sumatra and Borneo by the PCR-RFLP method. The SCAR marker did not amplify in Shorea parvifolia and thus can also be used to distinguish between S. leprosula and S. parvifolia. The marker was successfully amplified from wood DNA extracts suggesting its applicability to track the geographic origin of timber.

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“…In these databases, it is possible to fi nd all • kinds of sequences from any organism. The three main sequence databases are Genbank Nucleotide at the National Center for Biotechnology Information (NCBI) site (Benson et al 2011 ) , EMBL-Bank at the European Bioinformatics Institute (EBI) (Cochrane et al 2009 ) , and DNA Data Bank of Japan at the Center for Information Biology and DNA Databank (Kaminuma et al 2011 ) . These three databases share DNA sequence data and are a general data source for sequences for probe design.…”

Section: Microarray Probe Designmentioning

confidence: 99%

Bioinformatics in Support of Microarray Experiments

López-Campos

Martı́nez-Suárez

Aguado-Urda

et al. 2012

SpringerBriefs in Food, Health, and Nutrition

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For a long time, microarrays and bioinformatics have been intricately linked, and microarrays have emerged as a hot topic in the fi eld of bioinformatics. This happened due to the particularities of microarray technology, where huge amounts of information both are needed for the design of experiments and are generated from such experiments. Therefore, microarrays cannot be properly used or understood without considering all the bioinformatical aspects associated with them. This chapter is dedicated to describing the relevance and importance of bioinformatics in the development of microarray experiments. Microarray technology has to deal with massive amounts of information gathered from different sources during experimentation, such as samples, devices, methodologies, and eventually, experimental results. Therefore, microarray data management and analysis still remain among the most challenging aspects of microarray-based approaches and experiments.

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Petabyte-scale innovations at the European Nucleotide Archive

Cited by 83 publications

References 13 publications

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

Cultivation of hitherto-uncultured bacteria belonging to the Verrucomicrobia subdivision 1 from the potato (Solanum tuberosum L.) rhizosphere

Development of a diagnostic DNA marker for the geographic origin of Shorea leprosula

Bioinformatics in Support of Microarray Experiments

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