Construction of a robust microarray from a non‐model species largemouth bass, Micropterus salmoides (Lacèpede), using pyrosequencing technology

Abstract

A novel custom microarray for largemouth bass (Micropterus salmoides) was designed with sequences obtained from a normalized cDNA library using the 454 Life Sciences GS-20 pyrosequencer. This approach yielded in excess of 58 million bases of high-quality sequence. The sequence information was combined with 2,616 reads obtained by traditional suppressive subtractive hybridizations to derive a total of 31,391 unique sequences. Annotation and coding sequences were predicted for these transcripts where possible. 16,350 annotated transcripts were selected as target sequences for the design of the custom largemouth bass oligonucleotide microarray. The microarray was validated by examining the transcriptomic response in male largemouth bass exposed to 17beta-oestradiol. Transcriptomic responses were assessed in liver and gonad, and indicated gene expression profiles typical of exposure to oestradiol. The results demonstrate the potential to rapidly create the tools necessary to assess large scale transcriptional responses in non-model species, paving the way for expanded impact of toxicogenomics in ecotoxicology.

Applications of next generation sequencing in molecular ecology of non-model organisms

“…Traditionally this has been accomplished using microarrays (Kammenga et al, 2007), and has thus mainly been restricted to model species with previous genome information. However, as mentioned above, microarrays can now be constructed for nonmodel species using data from NGS transcriptome profiling (Garcia-Reyero et al, 2008), or used in a crossspecific way if developed in related genome reference species (Bar-Or et al, 2007). Development of microarrays through NGS considerably reduces both the cost and the effort involved.…”

Defining the role of omics in assessing ecosystem health: Perspectives from the Canadian environmental monitoring program

“…Although some gene ontologies such as macromolecular complex subunit organization and metabolic process were determined to be impacted at the molecular level in 3 or more field studies, the majority of gene ontology terms were represented only once or twice. Garcia-Reyero et al [83] determined that the main pathways upregulated in fish downstream of a sewage treatment plant included cell communication, signal transduction, and the protein kinase cascade, whereas down-regulated pathways included innate immune response and response to stress. Processes such as these should be examined in more detail in terms of LSI, condition, and food availability.…”

Endocrinology: Advances through omics and related technologies

“…The quality and quantity of sequence data generated by rapidly evolving sequencing techniques revolutionized research with non-model species, allowing researchers to construct high-quality microarrays for relevant species instead of focusing research efforts in model species. Such is the case of the development of a largemouth bass microarray (Garcia-Reyero et al, 2008), used to study estrogenic response in males; or a goldfish cDNA array (Martyniuk et al, 2006), used to study estrogenic effects on neuroendocrine function. The development of microarrays for non-model species though often faces the problem of poorly of annotated probes.…”