Genomic Organization of the B3-Domain Transcription Factor Family in Grapevine (Vitis vinifera L.) and Expression during Seed Development in Seedless and Seeded Cultivars

Abstract

Members of the plant-specific B3-domain transcription factor family have important and varied functions, especially with respect to vegetative and reproductive growth. Although B3 genes have been studied in many other plants, there is limited information on the genomic organization and expression of B3 genes in grapevine (Vitis vinifera L.). In this study, we identified 50 B3 genes in the grapevine genome and analyzed these genes in terms of chromosomal location and syntenic relationships, intron–exon organization, and promoter cis-element content. We also analyzed the presumed proteins in terms of domain structure and phylogenetic relationships. Based on the results, we classified these genes into five subfamilies. The syntenic relationships suggest that approximately half of the genes resulted from genome duplication, contributing to the expansion of the B3 family in grapevine. The analysis of cis-element composition suggested that most of these genes may function in response to hormones, light, and stress. We also analyzed expression of members of the B3 family in various structures of grapevine plants, including the seed during seed development. Many B3 genes were expressed preferentially in one or more structures of the developed plant, suggesting specific roles in growth and development. Furthermore, several of the genes were expressed differentially in early developing seeds from representative seeded and seedless cultivars, suggesting a role in seed development or abortion. The results of this study provide a foundation for functional analysis of B3 genes and new resources for future molecular breeding of grapevine.

PvB3s: Genome-wide and Transcriptome-wide Identification and Analysis Reveals the B3 Family Regulate Auxin to Resist Salt Stress at the Sprout Stage in Common Bean(P. Vulgaris L. ) .

“…Through evolutionary tree analysis, the B3 transcription factor family has been divided into 4 Subgroups, and the motifs, cis elements, and gene structures within each sub-group are very similar, indicating that each sub-group has PvB3s with similar functions; but the PvB3s among the four subgroups are very large In the analysis of the B3 transcription factors of Arabidopsis and the common bean (P. vulgaris L.) two species, they are divided into 4 subgroups according to the genetic relationship, and the members in each subgroup are similar in terms of motif or gene structure. This conclusion is consistent among citrus (C. sinensis and C. grandis) [36] and grapes (V. vinifera L.) [6].In tissue-speci c analysis, more PvB3s are expressed in the bud stage (whether ower buds, plant buds, or young pods) compared to other tissues. The same conclusion is found in grapes (V. vinifera L.) [37], citrus (C. sinensis and C. grandis) [36] and tobacco [38] (Nicotiana tabacum L.).…”

“…According to the domain structure and phylogenetic analysis, the B3 superfamily can be divided into four main families, namely, LAV (LEAFY COTYLE-DON2-ABAINSENSITIVE3-VAL), RAV (related to ABI3/VP1), ARF (auxin response factor) and REM (reproductive meristem) family. The B3 superfamily has found many model plants and crops in Arabidopsis, rice, poplar, rape, castor beans, cocoa, soybeans, corn, tobacco, grapes, moss, algae, citrus [3][4][5][6][7], but not foundings in common beans.…”

Genome-Wide Characterization and Expression Profiling of GASA Genes during Different Stages of Seed Development in Grapevine (Vitis vinifera L.) Predict Their Involvement in Seed Development

“…In the second method, the Hidden Markov Model (HMM) profile of the GASA domain (PFAM 02704) was used to search grapevine GASA proteins in the 12X coverage assembly of the V. vinifera PN40024 genome [40]. The NCBI Conserved Domain Database (https://www.ncbi.nlm.nih.gov/Structure/cdd/cdd.shtml) and Simple Modular Architecture Research Tool (SMART; http://smart.emblheidelberg.de/) were used to check the presence of the complete GASA domain in obtained protein sequences [41]. Finally, all non-redundant putative protein sequences with a conserved GASA domain were considered and used for further analysis.…”

Bioinformatics and Expression Analysis of Histone Modification Genes in Grapevine Predict Their Involvement in Seed Development, Powdery Mildew Resistance, and Hormonal Signaling

“…To identify a complete list of HMs genes in the grapevine, Hidden Markov Model (HMM) pro le of each gene family was downloaded from Pfam database (http://pfam.xfam.org/search#tabview=tab1) [31]. These HMM pro les were used as query against three public databases: Grape Genome Database (http://www.genoscope.cns.fr), the National Centre for Biotechnology Information (http://www.ncbi.nlm.nih.gov/), and the Grapevine Genome CRIBI Biotech website (http://genomes.cribi.unipd.it/) by HMMER software to nd full list of HMs proteins in grapevine [34].…”