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Deep analysis of wild Vitis flower transcriptome reveals unexplored genome regions associated with sex specification
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Orientador(es)
Resumo(s)
Key message 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.
Abstract 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
Descrição
Palavras-chave
Vitis vinifera ssp. sylvestris RNA-seq De novo assembly differential gene expression sex loci
Contexto Educativo
Citação
Plant Mol Biol (2017) 93:151–170
Editora
Springer