Comparison of cross-species and species-specific hybridizations. Solanum tuberosum

Abstract Background: One of the approaches for conducting genomics research in organisms that do not yet have a proper microarray template is to profile their expression patterns by using cross-species hybridization (CSH). Several different studies using spotted microarray for CSH resulted with contradicting conclusions as to the ability of CSH to reflect biological processes. Results: We used a tomato spotted cDNA microarray to examine the ability of CSH to reflect species specific hybridization (SSH) data. Potato RNA was hybridized to spotted cDNA tomato and potato microarrays to generate heterologous and homologous hybridization data, respectively. The results revealed difficulties in obtaining transcriptomics data from CSH that reflected those obtained from SSH. Nevertheless, once the data was filtered for those corresponding to matching probe sets, by restricting proper cutoffs of probe homology, the CSH transcriptomics data better reflected those of the SSH, to an extent that was quantitated by identification of differentially regulated genes. Conclusions: This study enabled us to outline some considerations regarding evaluation of a microarray as candidate platform for CSH study, performance of CSH and proper data analysis that may allow CSH to reflect to some extent a biological process. Keywords: cross-species hybridization; heterologous hybridization Overall design: To examine whether cross species hybridization (CSH) can produce data that reflects species specific hybridization (SSH) data, we used the same RNA samples for both CSH and SSH microarray experiments. RNA samples were extracted from nematode-infected and non-infected (control) potato plants, sampled at two time points (at 5 and at 10 days of nematode infection). These RNA samples were co-hybridized with a reference sample by CSH to a tomato microarray and by SSH to a potato microarray. The reference sample was pooled from all 8 samples (2 time points of infected or non-infected plants; 2 biological replicates were performed). The CSHs were designated as 'PT' for potato samples on tomato microarrays; the SSHs were designated as 'PP' for potato samples on potato microarrays.