Analysis of 13000 unique Citrus clusters associated with fruit quality, production and salinity tolerance
1 Centro de Genomica, Instituto Valenciano de Investigaciones Agrarias. Carretera Moncada – Náquera, Km. 4.5 Moncada (Valencia) E46113, Spain
2 BET-ITACA, Universidad Politécnica de Valencia, Camino de Vera, s/n 46022 Valencia, Spain
3 CIRAD AMIS, UMR PIA – Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France
4 Genoscope-Centre National de Séquençage and Centre National de la Recherche Scientifique (CNRS) Unité Mixte de Recherche (UMR)-8030, 91000 Evry, France
5 CIRAD FLHOR, UPR "Amélioration génétique d'espèces à multiplication végétative", Avenue Agropolis – TA 40/03 34398 Montpellier Cedex 5, France
BMC Genomics 2007, 8:31 doi:10.1186/1471-2164-8-31Published: 25 January 2007
Improvement of Citrus, the most economically important fruit crop in the world, is extremely slow and inherently costly because of the long-term nature of tree breeding and an unusual combination of reproductive characteristics. Aside from disease resistance, major commercial traits in Citrus are improved fruit quality, higher yield and tolerance to environmental stresses, especially salinity.
A normalized full length and 9 standard cDNA libraries were generated, representing particular treatments and tissues from selected varieties (Citrus clementina and C. sinensis) and rootstocks (C. reshni, and C. sinenis × Poncirus trifoliata) differing in fruit quality, resistance to abscission, and tolerance to salinity. The goal of this work was to provide a large expressed sequence tag (EST) collection enriched with transcripts related to these well appreciated agronomical traits. Towards this end, more than 54000 ESTs derived from these libraries were analyzed and annotated. Assembly of 52626 useful sequences generated 15664 putative transcription units distributed in 7120 contigs, and 8544 singletons. BLAST annotation produced significant hits for more than 80% of the hypothetical transcription units and suggested that 647 of these might be Citrus specific unigenes. The unigene set, composed of ~13000 putative different transcripts, including more than 5000 novel Citrus genes, was assigned with putative functions based on similarity, GO annotations and protein domains
Comparative genomics with Arabidopsis revealed the presence of putative conserved orthologs and single copy genes in Citrus and also the occurrence of both gene duplication events and increased number of genes for specific pathways. In addition, phylogenetic analysis performed on the ammonium transporter family and glycosyl transferase family 20 suggested the existence of Citrus paralogs. Analysis of the Citrus gene space showed that the most important metabolic pathways known to affect fruit quality were represented in the unigene set. Overall, the similarity analyses indicated that the sequences of the genes belonging to these varieties and rootstocks were essentially identical, suggesting that the differential behaviour of these species cannot be attributed to major sequence divergences. This Citrus EST assembly contributes both crucial information to discover genes of agronomical interest and tools for genetic and genomic analyses, such as the development of new markers and microarrays.