title: Inspection of the grapevine BURP superfamily highlights an expansion of RD22 genes with distinctive expression features in berry development and ABA-mediated stress responses.
abstract: The RESPONSIVE TO DEHYDRATION 22 (RD22) gene is a molecular link between abscisic acid (ABA) signalling and abiotic stress responses. Its expression has been used as a reliable ABA early response marker. In Arabidopsis, the single copy RD22 gene possesses a BURP domain also located at the C-terminus of USP embryonic proteins and the beta subunit of polygalacturonases. In grapevine, a RD22 gene has been identified but putative paralogs are also found in the grape genome, possibly forming a large RD22 family in this species. In this work, we searched for annotations containing BURP domains in the Vitis vinifera genome. Nineteen proteins were defined by a comparative analysis between the two genome predictions and RNA-Seq data. These sequences were compared to other plant BURPs identified in previous genome surveys allowing us to reconceive group classifications based on phylogenetic relationships and protein motif occurrence. We observed a lineage-specific evolution of the RD22 family, with the biggest expansion in grapevine and poplar. In contrast, rice, sorghum and maize presented highly expanded monocot-specific groups. The Vitis RD22 group may have expanded from segmental duplications as most of its members are confined to a region in chromosome 4. The inspection of transcriptomic data revealed variable expression of BURP genes in vegetative and reproductive organs. Many genes were induced in specific tissues or by abiotic and biotic stresses. Three RD22 genes were further studied showing that they responded oppositely to ABA and to stress conditions. Our results show that the inclusion of RNA-Seq data is essential while describing gene families and improving gene annotations. Robust phylogenetic analyses including all BURP members from other sequenced species helped us redefine previous relationships that were erroneously established. This work provides additional evidence for RD22 genes serving as marker genes for different organs or stresses in grapevine.
authors.affiliation: Center for Research in Agricultural Genomics CSIC-IRTA-UAB-UB, Bellaterra, Barcelona, Spain; Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: José Tomás
authors.initials: JT
authors.lastname: Matus
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Felipe
authors.initials: F
authors.lastname: Aquea
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Carmen
authors.initials: C
authors.lastname: Espinoza
authors.affiliation: Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Andrea
authors.initials: A
authors.lastname: Vega
authors.affiliation: Department of Biotechnology, University of Verona, Verona, Italy.
authors.forename: Erika
authors.initials: E
authors.lastname: Cavallini
authors.affiliation: Department of Biotechnology, University of Verona, Verona, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Dal Santo
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Paola
authors.initials: P
authors.lastname: Cañón
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Amparo
authors.initials: A
authors.lastname: Rodríguez-Hoces de la Guardia
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Serrano
authors.affiliation: Department of Biotechnology, University of Verona, Verona, Italy.
authors.forename: Giovanni Battista
authors.initials: GB
authors.lastname: Tornielli
authors.affiliation: Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago, Chile.
authors.forename: Patricio
authors.initials: P
authors.lastname: Arce-Johnson
mesh_terms: D000040:Abscisic Acid / Q000378:metabolism*; D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics; D029681:Arabidopsis Proteins / Q000096:biosynthesis / Q000235:genetics; D003681:Dehydration / Q000235:genetics; D005638:Fruit / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D018506:Gene Expression Regulation, Plant; D005810:Multigene Family; D010802:Phylogeny; D017423:Sequence Analysis, RNA; D013312:Stress, Physiological / Q000235:genetics*; D027843:Vitis / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; C080922:RD22 protein, Arabidopsis; D000040:Abscisic Acid