A genome-wide 20 K citrus microarray for gene expression analysis.
BACKGROUND
Understanding of genetic elements that contribute to key aspects of citrus biology will impact future improvements in this economically important crop. Global gene expression analysis demands microarray platforms with a high genome coverage. In the last years, genome-wide EST collections have been generated in citrus, opening the possibility to create new tools for functional genomics in this crop plant.


RESULTS
We have designed and constructed a publicly available genome-wide cDNA microarray that include 21,081 putative unigenes of citrus. As a functional companion to the microarray, a web-browsable database 1 was created and populated with information about the unigenes represented in the microarray, including cDNA libraries, isolated clones, raw and processed nucleotide and protein sequences, and results of all the structural and functional annotation of the unigenes, like general description, BLAST hits, putative Arabidopsis orthologs, microsatellites, putative SNPs, GO classification and PFAM domains. We have performed a Gene Ontology comparison with the full set of Arabidopsis proteins to estimate the genome coverage of the microarray. We have also performed microarray hybridizations to check its usability.


CONCLUSIONS
This new cDNA microarray replaces the first 7K microarray generated two years ago and allows gene expression analysis at a more global scale. We have followed a rational design to minimize cross-hybridization while maintaining its utility for different citrus species. Furthermore, we also provide access to a website with full structural and functional annotation of the unigenes represented in the microarray, along with the ability to use this site to directly perform gene expression analysis using standard tools at different publicly available servers. Furthermore, we show how this microarray offers a good representation of the citrus genome and present the usefulness of this genomic tool for global studies in citrus by using it to catalogue genes expressed in citrus globular embryos.
Martinez-Godoy
M Angeles
MA
Instituto de Biología Molecular y Celular de Plantas (IBMCP), Laboratorio de Genomica (Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas), Avenida de los Naranjos s/n, E46022 Valencia, Spain. mmargodo@ibmcp.upv.es
Mauri
Nuria
N
Juarez
Jose
J
Marques
M Carmen
MC
Santiago
Julia
J
Forment
Javier
J
Gadea
Jose
J
D017360:Arabidopsis / Q000235:genetics; D001483:Base Sequence; D002957:Citrus / Q000235:genetics*; D016000:Cluster Analysis; D018076:DNA, Complementary / Q000737:chemistry / Q000235:genetics; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D020224:Expressed Sequence Tags; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D015723:Gene Library; D005819:Genetic Markers; D018745:Genome, Plant; D020407:Internet; D018895:Microsatellite Repeats; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020641:Polymorphism, Single Nucleotide; D017434:Protein Structure, Tertiary; D018749:RNA, Plant; D020539:Sequence Analysis, Protein
D018076:DNA, Complementary; D005819:Genetic Markers; D018749:RNA, Plant