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Analysis of institutional authors

Martinez-Godoy, MaAuthorForment, JAuthorGadea, JCorresponding Author

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October 29, 2024
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A genome-wide 20 K citrus microarray for gene expression analysis

Publicated to:Bmc Genomics. 9 318- - 2008-07-03 9(), DOI: 10.1186/1471-2164-9-318

Authors: Martinez-Godoy, M Angeles; Mauri, Nuria; Juarez, Jose; Marques, M Carmen; Santiago, Julia; Forment, Javier; Gadea, Jose

Affiliations

Inst Valenciano Invest Agr - Author
Univ Politecn Valencia, Consejo Super Invest Cientificas, Lab Genom, Inst Biol Mol & Celular Plantas - Author

Abstract

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 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. 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.

Keywords

Amino acid sequenceArabidopsisArabidopsis proteinArticleBase sequenceCdna microarrayChemistryCitrusCitrus fruitCloneCluster analysisComplementary dnaControlled studyCross hybridizationData interpretation, statisticalDatabases, factualDna libraryDna microarrayDna, complementaryExpressed sequence tagExpressed sequence tagsFactual databaseFunctional genomicsGene expression profilingGene expression regulationGene expression regulation, plantGene libraryGenetic databaseGenetic markerGenetic markersGeneticsGenomeGenome analysisGenome, plantInternetMethodologyMicroarray analysisMicrosatellite dnaMicrosatellite markerMicrosatellite repeatsNonhumanNucleotideNucleotide sequenceOligonucleotide array sequence analysisOrthologyPattern-formationPlant geneticsPlant rnaPolymorphism, single nucleotideProteinProtein domainProtein processingProtein structure, tertiaryProtein tertiary structureQualityResourcesRna, plantSequence analysisSequence analysis, proteinSingle nucleotide polymorphismStatistical analysisToolTranscriptomeUnindexed sequence

Quality index

Bibliometric impact. Analysis of the contribution and dissemination channel

The work has been published in the journal Bmc Genomics due to its progression and the good impact it has achieved in recent years, according to the agency WoS (JCR), it has become a reference in its field. In the year of publication of the work, 2008, it was in position 24/144, thus managing to position itself as a Q1 (Primer Cuartil), in the category Biotechnology & Applied Microbiology.

From a relative perspective, and based on the normalized impact indicator calculated from the Field Citation Ratio (FCR) of the Dimensions source, it yields a value of: 3.2, which indicates that, compared to works in the same discipline and in the same year of publication, it ranks as a work cited above average. (source consulted: Dimensions Sep 2025)

Specifically, and according to different indexing agencies, this work has accumulated citations as of 2025-09-07, the following number of citations:

  • WoS: 48
  • Scopus: 51

Impact and social visibility

From the perspective of influence or social adoption, and based on metrics associated with mentions and interactions provided by agencies specializing in calculating the so-called "Alternative or Social Metrics," we can highlight as of 2025-09-07:

  • The use of this contribution in bookmarks, code forks, additions to favorite lists for recurrent reading, as well as general views, indicates that someone is using the publication as a basis for their current work. This may be a notable indicator of future more formal and academic citations. This claim is supported by the result of the "Capture" indicator, which yields a total of: 63 (PlumX).

It is essential to present evidence supporting full alignment with institutional principles and guidelines on Open Science and the Conservation and Dissemination of Intellectual Heritage. A clear example of this is:

  • The work has been submitted to a journal whose editorial policy allows open Open Access publication.

Leadership analysis of institutional authors

There is a significant leadership presence as some of the institution’s authors appear as the first or last signer, detailed as follows: First Author (Martínez Godoy, Mª Angeles) and Last Author (Gadea Vacas, José).

the author responsible for correspondence tasks has been Gadea Vacas, José.