The grapevine gene nomenclature system

Background

Grapevine (Vitis vinifera L.) is one of the most important fruit crops in the world and serves as a valuable model for fruit development in woody species. A major breakthrough in grapevine genomics was achieved in 2007 with the sequencing of the Vitis vinifera cv. PN40024 genome. Subsequently, data on structural and functional characterization of grape genes accumulated exponentially. To better exploit the results obtained by the international community, we think that a coordinated nomenclature for gene naming in species with sequenced genomes is essential. It will pave the way for the accumulation of functional data that will enable effective scientific discussion and discovery. The exploitation of data that were generated independently of the genome release is hampered by their heterogeneous nature and by often incompatible and decentralized storage. Classically, large amounts of data describing gene functions are only available in printed articles and therefore remain hardly accessible for automatic text mining. On the other hand, high throughput “Omics” data are typically stored in public repositories, but should be arranged in compendia to better contribute to the annotation and functional characterization of the genes.

Results

With the objective of providing a high quality and highly accessible annotation of grapevine genes, the International Grapevine Genome Project (IGGP) commissioned an international Super-Nomenclature Committee for Grape Gene Annotation (sNCGGa) to coordinate the effort of experts to annotate the grapevine genes. The goal of the committee is to provide a standard nomenclature for locus identifiers and to define conventions for a gene naming system in this paper.

Conclusions

Learning from similar initiatives in other plant species such as Arabidopsis, rice and tomato, a versatile nomenclature system has been developed in anticipation of future genomic developments and annotation issues. The sNCGGa’s first outreach to the grape community has been focused on implementing recommended guidelines for the expert annotators by: (i) providing a common annotation platform that enables community-based gene curation, (ii) developing a gene nomenclature scheme reflecting the biological features of gene products that is consistent with that used in other organisms in order to facilitate comparative analyses.     

Genome-Wide Analysis of the Expansin Gene Superfamily Reveals Grapevine-Specific Structural and Functional Characteristics

Background

Expansins are proteins that loosen plant cell walls in a pH-dependent manner, probably by increasing the relative movement among polymers thus causing irreversible expansion. The expansin superfamily (EXP) comprises four distinct families: expansin A (EXPA), expansin B (EXPB), expansin-like A (EXLA) and expansin-like B (EXLB). There is experimental evidence that EXPA and EXPB proteins are required for cell expansion and developmental processes involving cell wall modification, whereas the exact functions of EXLA and EXLB remain unclear. The complete grapevine (Vitis vinifera) genome sequence has allowed the characterization of many gene families, but an exhaustive genome-wide analysis of expansin gene expression has not been attempted thus far.

Methodology/Principal Findings

We identified 29 EXP superfamily genes in the grapevine genome, representing all four EXP families. Members of the same EXP family shared the same exon–intron structure, and phylogenetic analysis confirmed a closer relationship between EXP genes from woody species, i.e. grapevine and poplar (Populus trichocarpa), compared to those from Arabidopsis thaliana and rice (Oryza sativa). We also identified grapevine-specific duplication events involving the EXLB family. Global gene expression analysis confirmed a strong correlation among EXP genes expressed in mature and green/vegetative samples, respectively, as reported for other gene families in the recently-published grapevine gene expression atlas. We also observed the specific co-expression of EXLB genes in woody organs, and the involvement of certain grapevine EXP genes in berry development and post-harvest withering.

Conclusion

Our comprehensive analysis of the grapevine EXP superfamily confirmed and extended current knowledge about the structural and functional characteristics of this gene family, and also identified properties that are currently unique to grapevine expansin genes. Our data provide a model for the functional characterization of grapevine gene families by combining phylogenetic analysis with global gene expression profiling.     

Upregulation of two ripening‐related genes from a non‐climacteric plant (pepper) in a transgenic climacteric plant (tomato)

Activities of promoters from the capsanthin/capsorubin synthase and fibrillin genes, which are molecular markers for ripening in the non-climacteric pepper fruits, have been studied in transgenic tomato plants that produce fruits of the climacteric type (characterized by an increase in respiration and ethylene production). The promoters of both genes were strongly upregulated during tomato fruit ripening in a manner similar to the induction of these genes in pepper fruits. Induction occurred at the mature green stage preceding ripening (a stage when ethylene production and respiration are known to rise in tomato fruits). Ethylene positively influenced the expression of both genes in tomato. Other plant growth regulators, namely abscisic acid, auxin and polyamines, did not alter gene expression. In contrast, water loss strongly induced both promoters. This dehydration-mediated gene induction was inhibited by mitochondrial respiration inhibitors (mainly of the alternative oxidase). A slight positive effect with light, apparently not linked to normal photosynthesis but rather to photooxidative stress, was also observed. Taken together, the data indicate that activation of oxidase systems, leading to changes in the cellular redox balance, mediates the induction of both genes in tomato. Various cellular compartments are likely to be contributors to this process, which leads to the developmental regulation of nuclear genes encoding plastid-located proteins.     

Novel promoters that induce specific transgene expression during the green to ripening stages of tomato fruit development

Fruit-specific promoters have been used as genetic engineering tools for studies on molecular mechanism of fruit development and advance in fruit quality and additional value by increasing functional component. Especially fruit-ripening specific promoters have been well utilized and studied in tomato; however, few studies have reported the development of promoters that act at fruit developing stages such as immature green and mature green periods. In this study, we report novel promoters for gene expression during the green to ripening stages of tomato fruit development. Genes specifically expressed at tomato fruit were selected using microarray data. Subsequent to confirmation of the expression of the selected 12 genes, upstream DNA fragments of the genes LA22CD07, Les.3122.2.A1_a_at and LesAffx.6852.1.S1_at which specifically expressed at fruit were isolated from tomato genomic DNA as promoter regions. Isolated promoter regions were fused with the GUS gene and the resultant constructs were introduced into tomato by agrobacterium-mediated transformation for evaluation of promoter activity in tomato fruit. The two promoters of LA22CD07, and LesAffx.6852.1.S1_at showed strong activity in the fruit, weak activity in the flower and undetectable activity in other tissues. Unlike well-known fruit-ripening specific promoters, such as the E8 promoter, these promoters exhibited strong activity in green fruit in addition to red-ripening fruit, indicating that the promoters are suitable for transgene expression during green to ripening stages of tomato fruit development. KEY MESSAGE: Novel fruit-specific promoters have been identified and are suitable for transgene expression during green to ripening stages of tomato fruit development.