Methodology article
Derivation of species-specific hybridization-like knowledge out of cross-species hybridization results
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* Corresponding author: Hinanit Koltai hkoltai@agri.gov.il
1 Department of Ornamental Horticulture, ARO Volcani Center, Bet Dagan, Israel
2 Department of Nematology, ARO Volcani Center, Bet Dagan, Israel
3 Depatment of Agronomy & Natural Resources, ARO Volcani Center, Bet Dagan, Israel
4 The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture of the Hebrew University of Jerusalem, Rehovot, Israel
BMC Genomics 2006, 7:110 doi:10.1186/1471-2164-7-110
Published: 8 May 2006Abstract
Background
One of the approaches for conducting genomics research in organisms without extant microarray platforms is to profile their expression patterns by using Cross-Species Hybridization (CSH). Several different studies using spotted microarray and CSH produced contradicting conclusions in the ability of CSH to reflect biological processes described by species-specific hybridization (SSH).
Results
We used a tomato-spotted cDNA microarray to examine the ability of CSH to reflect SSH data. Potato RNA was hybridized to spotted cDNA tomato and potato microarrays to generate CSH and SSH data, respectively. Difficulties arose in obtaining transcriptomic 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 transcriptome data showed improved reflection of those of the SSH.
Conclusions
This study evaluated the relative performance of CSH compared to SSH, and proposes methods to ensure that CSH closely reflects the biological process analyzed by SSH.