2024-03-19T03:12:26Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/479342021-12-27T15:32:49Zcom_10261_103com_10261_1col_10261_356
2012-04-04T11:15:24Z
urn:hdl:10261/47934
A genome-wide 20 K citrus microarray for gene expression analysis
Martínez-Godoy, M. Ángeles
Mauri, Nuria
Juárez, José
Marqués, M. Carmen
Santiago, Julia
Forment, Javier
Gadea Vacas, José
Plant Embriogenesis
Pattern-formation
cDNA microarrays
Tool
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, genomewide
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 webbrowsable
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.
Conclusion: 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.
2012-04-04T11:15:24Z
2012-04-04T11:15:24Z
2008-07-03
artículo
BMC Genomics 9:318 (2008)
http://hdl.handle.net/10261/47934
10.1186/1471-2164-9-318
1471-2164
18598343
eng
Publisher’s version
openAccess
BioMed Central