title: Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification.
abstract: RNA-seq of Vitis during early stages of bud development, in male, female and hermaphrodite flowers, identified new loci outside of annotated gene models, suggesting their involvement in sex establishment. The molecular mechanisms responsible for flower sex specification remain unclear for most plant species. In the case of V. vinifera ssp. vinifera, it is not fully understood what determines hermaphroditism in the domesticated subspecies and male or female flowers in wild dioecious relatives (Vitis vinifera ssp. sylvestris). Here, we describe a de novo assembly of the transcriptome of three flower developmental stages from the three Vitis vinifera flower types. The validation of de novo assembly showed a correlation of 0.825. The main goals of this work were the identification of V. v. sylvestris exclusive transcripts and the characterization of differential gene expression during flower development. RNA from several flower developmental stages was used previously to generate Illumina sequence reads. Through a sequential de novo assembly strategy one comprehensive transcriptome comprising 95,516 non-redundant transcripts was assembled. From this dataset 81,064 transcripts were annotated to V. v. vinifera reference transcriptome and 11,084 were annotated against V. v. vinifera reference genome. Moreover, we found 3368 transcripts that could not be mapped to Vitis reference genome. From all the non-redundant transcripts that were assembled, bioinformatics analysis identified 133 specific of V. v. sylvestris and 516 transcripts differentially expressed among the three flower types. The detection of transcription from areas of the genome not currently annotated suggests active transcription of previously unannotated genomic loci during early stages of bud development.
authors: Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
authors: Miguel Jesus Nunes
authors: MJ
authors: Ramos
authors: Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
authors: João Lucas
authors: JL
authors: Coito
authors: Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
authors: Joana
authors: J
authors: Fino
authors: Instituto Nacional de Investigação Agrária e Veterinária, Quinta d'Almoinha, Dois Portos, Portugal.|Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa, Oeiras, Portugal.
authors: Jorge
authors: J
authors: Cunha
authors: BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors: Helena
authors: H
authors: Silva
authors: Development and Evolutionary Morphogenesis, Centre for Ecology, Evolution and Environmental Change, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
authors: Patrícia Gomes
authors: PG
authors: de Almeida
authors: BioSystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Centre, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal.
authors: Maria Manuela Ribeiro
authors: MM
authors: Costa
authors: Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal.
authors: Sara
authors: S
authors: Amâncio
authors: Computational Biology and Population Genomics Group, Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal.
authors: Octávio S
authors: OS
authors: Paulo
authors: Universidade de Lisboa, Instituto Superior de Agronomia, LEAF, Linking Landscape, Environment, Agriculture and Food, Tapada da Ajuda, 1359-017, Lisboa, Portugal. rocheta@isa.ulisboa.pt.
authors: Margarida
authors: http://orcid.org/0000-0003-3939-4564
authors: M
authors: Rocheta
mesh_terms: D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D035264:Flowers / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D018745:Genome, Plant; D010937:Plant Growth Regulators / Q000235:genetics / Q000378:metabolism; D010940:Plant Proteins / Q000235:genetics / Q000378:metabolism; D012098:Reproduction; D019849:Sex Determination Processes; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D059467:Transcriptome; D027843:Vitis / Q000235:genetics* / Q000378:metabolism / Q000502:physiology
chemical_list: D010937:Plant Growth Regulators; D010940:Plant Proteins; D014157:Transcription Factors
keywords: De novo assembly; Differential gene expression; RNA-seq; Sex loci; Vitis vinifera ssp. sylvestris