Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE).

PloS One
Sara C NovaisMónica J B Amorim

Abstract

Enchytraeus albidus (Oligochaeta) is an ecologically relevant species used as standard test organisms for risk assessment. Effects of stressors in this species are commonly determined at the population level using reproduction and survival as endpoints. The assessment of transcriptomic responses can be very useful e.g. to understand underlying mechanisms of toxicity with gene expression fingerprinting. In the present paper the following is being addressed: 1) development of suppressive subtractive hybridization (SSH) libraries enriched for differentially expressed genes after metal and pesticide exposures; 2) sequencing and characterization of all generated cDNA inserts; 3) development of a publicly available genomic database on E. albidus. A total of 2100 Expressed Sequence Tags (ESTs) were isolated, sequenced and assembled into 1124 clusters (947 singletons and 177 contigs). From these sequences, 41% matched known proteins in GenBank (BLASTX, e-value ≤ 10(-5)) and 37% had at least one Gene Ontology (GO) term assigned. In total, 5.5% of the sequences were assigned to a metabolic pathway, based on KEGG. With this new sequencing information, an Agilent custom oligonucleotide microarray was designed, representing a potential tool...Continue Reading

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Citations

Jun 14, 2014·Metallomics : Integrated Biometal Science·J G Bundy, P Kille
Dec 24, 2013·Environmental Pollution·Susana I L GomesMónica J B Amorim

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Methods Mentioned

BETA
EST
PCR

Software Mentioned

CodonCode Aligner
Basic Local Alignment Search Tool ( BLAST )
PostgreSQL
PartiGene
blastn
Cap3
wwwPartiGene
Evrogen
EnchyBASE
blastx

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