title: CoffeebEST: an integrated resource for Coffea spp expressed sequence tags.
abstract: Coffee is one of the most important commodities in the world, and its production relies mainly on two species, Coffea arabica and Coffea canephora. Although there are diverse transcriptome datasets available for coffee trees, few research groups have exploited the potential knowledge contained in these data, especially with respect to fruit and seed development. Here, we present a comparative analysis of the transcriptomes of Coffea arabica and Coffea canephora with a focus on fruit development using publicly available expressed sequence tags (ESTs). Most of the fruit and seed EST data has been obtained from C. canephora. Therefore, we performed a fruit EST analysis of the 5 developmental stages of this species (18, 22, 30, 42, and 46 weeks after flowering) comprising 29,009 sequences. We compared C. canephora fruit ESTs to reference unigenes of C. canephora (7710 contigs and 8955 singletons) and C. arabica (15,656 contigs and 16,351 singletons). Additional analyses included functional annotation based on Gene Onthology, as well as an annotation using PlantCyc, a curated plant protein database. The Coffee Bean EST (CoffeebEST) is a public database available at http://bioinfo-02.cp.utfpr.edu.br/. This database represents an additional resource for the coffee scientific community, offering a user-friendly collection of information for non-specialists in coffee molecular biology to support experimental research on comparative and functional genomics.
authors.affiliation: Universidade Tecnológica Federal do Paraná, Cornélio Procópio, PR, Brasil.
authors.forename: A R
authors.initials: AR
authors.lastname: Paschoal
authors.affiliation: Universidade Tecnológica Federal do Paraná, Cornélio Procópio, PR, Brasil.
authors.forename: E D M
authors.initials: ED
authors.lastname: Fernandes
authors.affiliation: Universidade Tecnológica Federal do Paraná, Cornélio Procópio, PR, Brasil.
authors.forename: J C
authors.initials: JC
authors.lastname: Silva
authors.affiliation: Universidade Tecnológica Federal do Paraná, Cornélio Procópio, PR, Brasil.
authors.forename: F M
authors.initials: FM
authors.lastname: Lopes
authors.affiliation: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, PR, Brasil.
authors.forename: L F P
authors.initials: LF
authors.lastname: Pereira
authors.affiliation: Laboratório de Biotecnologia Vegetal, Instituto Agronômico do Paraná, Londrina, PR, Brasil doug@iapar.br.
authors.forename: D S
authors.initials: DS
authors.lastname: Domingues
mesh_terms: D040503:Coffea / Q000145:classification* / Q000235:genetics* / Q000254:growth & development; D019295:Computational Biology / Q000379:methods*; D020224:Expressed Sequence Tags; D005638:Fruit / Q000235:genetics / Q000254:growth & development; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D018506:Gene Expression Regulation, Plant; D058977:Molecular Sequence Annotation; D010940:Plant Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA; D012984:Software; D059467:Transcriptome
chemical_list: D010940:Plant Proteins