Abstract
Seedless grapes are of considerable importance for the raisin and table grape industries. Previous transcriptome analyses of seed development in grape revealed that genes encoding homeobox transcription factors were differentially regulated in seedless compared with seeded grape during seed development. In the present study, we identified a total of 73 homeobox-like genes in the grapevine genome and analyzed the genomic content and expression profiles of these genes. Based on domain architecture and phylogenetic analyses grape homeobox genes can be classified into eleven subfamilies. An analysis of the exon-intron structures and conserved motifs provided further insight into the evolutionary relationships between these genes. Evaluation of synteny indicated that segmental and tandem duplications have contributed greatly to the expansion of the grape homeobox gene superfamily. Synteny analysis between the grape and Arabidopsis genomes provided a potential functional relevance for these genes. The tissue-specific expression patterns of homeobox genes suggested roles in both vegetative and reproductive tissues. Expression profiling of these genes during the course of ovule development in seeded and seedless cultivars suggested a potential role in ovule abortion associated with seedlessness. This study will facilitate the functional analysis of these genes and provide new resources for molecular breeding of seedless grapes.
Highlights
Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes
We identified a total of 73 HB genes. These genes were designated as Vitis vinifera HB (VvHB) 1–73 based on their chromosomal positions (Table 1)
Relating these syntenies to the phylogenetic analysis (Fig. 1), we discovered each pair of genes from grape and Arabidopsis belongs to the same subfamily (Supplementary Table S5), some of these gene pairs even cluster in the same phylogenetic subclade, suggesting that many VvHB genes share a common ancestor with their Arabidopsis counterpart, and that they may have the closest genetic relationship
Summary
Genome-wide identification and expression analyses of the homeobox transcription factor family during ovule development in seedless and seeded grapes. Homeobox (HB) transcription factors often act as master regulators of organ identity and are encoded by a large and conserved gene family. These were originally characterized as regulators of morphogenesis in the fruit fly, Drosophila melanogaster[1]. The second and third helices form a helix-turn-helix motif, which can interact with specific DNA sequences, allowing for regulation of expression of target genes[10,11]. Based on the conserved sequence of the HD along with other characteristic domains and motifs, HB genes are classified into 14 families[12], including HD-ZIP I-IV, KNOX, WOX, PHD, NDX, BEL, PLINC, DDT, LD, SAWADEE and PINTOX. Each HB gene family is named according to unique typical domains and motifs outside of the HD, features that may enable functional differences of each subfamily
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