title: Plant genome and transcriptome annotations: from misconceptions to simple solutions.
abstract: Next-generation sequencing has triggered an explosion of available genomic and transcriptomic resources in the plant sciences. Although genome and transcriptome sequencing has become orders of magnitudes cheaper and more efficient, often the functional annotation process is lagging behind. This might be hampered by the lack of a comprehensive enumeration of simple-to-use tools available to the plant researcher. In this comprehensive review, we present (i) typical ontologies to be used in the plant sciences, (ii) useful databases and resources used for functional annotation, (iii) what to expect from an annotated plant genome, (iv) an automated annotation pipeline and (v) a recipe and reference chart outlining typical steps used to annotate plant genomes/transcriptomes using publicly available resources.
authors.affiliation: Forschungszentrum Jülich, Wilhelm Johnen Str, 52428, Jülich, Germany.
authors.forename: Marie E
authors.initials: ME
authors.lastname: Bolger
authors.affiliation: Forschungszentrum Jülich, Wilhelm Johnen Str, 52428, Jülich, Germany.|FRS-FNRS Chargé de Recherches, Functional Genomics and Plant Molecular Imaging Center for Protein Engineering (CIP), Dpt of Life Sciences, University of Liège, Quartier de la Vallée, 1, Chemin de la Vallée, 4 - Bât B22, 4000 LIEGE, Belgium.
authors.forename: Borjana
authors.initials: B
authors.lastname: Arsova
authors.affiliation: Forschungszentrum Jülich, Wilhelm Johnen Str, 52428, Jülich, Germany.|RWTH Aachen University, Institute for Biology I Botany, BioSC, Worringer Weg 3, 52078 Aachen, Germany.
authors.forename: Björn
authors.initials: B
authors.lastname: Usadel
mesh_terms: D018745:Genome, Plant; D023281:Genomics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D058977:Molecular Sequence Annotation / Q000379:methods*; D010940:Plant Proteins / Q000235:genetics*; D010944:Plants / Q000235:genetics*; D012984:Software; D059467:Transcriptome
chemical_list: D010940:Plant Proteins