Genes In Tomato Genome Research Articles

Deeper genomic insights into tomato CLE genes repertoire identify new active peptides

BackgroundIn eukaryotes, cell-to-cell communication relies on the activity of small signaling peptides. In plant genomes, many hundreds of genes encode for such short peptide signals. However, only few of them are functionally characterized and due to the small gene size and high sequence variability, the comprehensive identification of such peptide-encoded genes is challenging. The CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION-RELATED (CLE) gene family encodes for short peptides that have a role in plant meristem maintenance, vascular patterning and responses to environment. The full repertoire of CLE genes and the role of CLE signaling in tomato (Solanum lycopersicum)- one of the most important crop plants- has not yet been fully studied.ResultsBy using a combined approach, we performed a genome-wide identification of CLE genes using the current tomato genome version SL 4.0. We identified 52 SlCLE genes, including 37 new non annotated before. By analyzing publicly available RNAseq datasets we could confirm the expression of 28 new SlCLE genes. We found that SlCLEs are often expressed in a tissue-, organ- or condition-specific manner. Our analysis shows an interesting gene diversification within the SlCLE family that seems to be a result of gene duplication events. Finally, we could show a biological activity of selected SlCLE peptides in the root growth arrest that was SlCLV2-dependent.ConclusionsOur improved combined approach revealed 37 new SlCLE genes. These findings are crucial for better understanding of the CLE signaling in tomato. Our phylogenetic analysis pinpoints the closest homologs of Arabidopsis CLE genes in tomato genome and can give a hint about the function of newly identified SlCLEs. The strategy described here can be used to identify more precisely additional short genes in plant genomes. Finally, our work suggests that the mechanism of root-active CLE peptide perception is conserved between Arabidopsis and tomato. In conclusion, our work paves the way to further research on the CLE-dependent circuits modulating tomato development and physiological responses.

Light and ripening-regulated BBX protein-encoding genes in Solanum lycopersicum

Light controls several aspects of plant development through a complex signalling cascade. Several B-box domain containing proteins (BBX) were identified as regulators of Arabidopsis thaliana seedling photomorphogenesis. However, the knowledge about the role of this protein family in other physiological processes and species remains scarce. To fill this gap, here BBX protein encoding genes in tomato genome were characterised. The robust phylogeny obtained revealed how the domain diversity in this protein family evolved in Viridiplantae and allowed the precise identification of 31 tomato SlBBX proteins. The mRNA profiling in different organs revealed that SlBBX genes are regulated by light and their transcripts accumulation is directly affected by the chloroplast maturation status in both vegetative and fruit tissues. As tomato fruits develops, three SlBBXs were found to be upregulated in the early stages, controlled by the proper chloroplast differentiation and by the PHYTOCHROME (PHY)-dependent light perception. Upon ripening, other three SlBBXs were transcriptionally induced by RIPENING INHIBITOR master transcriptional factor, as well as by PHY-mediated signalling and proper plastid biogenesis. Altogether, the results obtained revealed a conserved role of SlBBX gene family in the light signalling cascade and identified putative members affecting tomato fruit development and ripening.

Whirly (Why) transcription factors in tomato (Solanum lycopersicum L.): genome-wide identification and transcriptional profiling under drought and salt stresses

Whirly (Why) transcription factor (TFs) constitute one of the important TF families which plays essential roles in plant metabolism to cope with environmental stresses. In the present study, Why genes were identified at genome-wide scale in tomato (Solanum lycopersicum), and bioinformatics analyses were implemented. Validation of Why genes expressions under drought and salt stresses were also performed using RT-qPCR. The analyses revealed the presence of two Why genes in tomato genome, SlWhy1 (Solyc05g007100.2.1) and SlWhy2 (Solyc11g044750.1.1). Both genes contained Whirly transcription factor domain structure (PF08536), and Why proteins were in basic character (pI ≥ 7). While the lengths of the proteins ranged from 268 to 236 amino acid residues for SlWhy1 and SlWhy2 respectively, exon numbers identified in both genes were seven. According to the digital expression data, SlWhy genes are expressed at medium level in different anatomical parts and developmental stages. In the promotor sequence analysis, 13 types of putative TF binding sites were identified, and the highest motif number was 46, found for GATA TF. Gene co-expression analyses revealed that complex networks for SlWhy genes, which are connected with various metabolic pathways. Based on the RT-qPCR data, both SlWhy1 and SlWhy2 genes were up-regulated under salt and drought stresses. 3D structure analyses revealed that SlWhy1 protein had a more diverged structure than SlWhy2 protein, based on their comparisons in Arabidopsis and potato. The results obtained in the present study could be a useful scientific basis for understanding Why genes in tomato and their functions under abiotic stress conditions.

Microarray analysis for the influence of CMV infection on tomato genomes (617.1)

Functional genomics is the study of gene function through parallel expression measurements of a genome. The most common tools used to carry out these measurements include complementary DNA microarrays, oligonucleotide microarrays or serial analysis of gene expression (SAGE)3. A custom‐designed Affymetrix tomato GeneChip array was used to study the gene expression changes in response to viral inoculation with a mild and severe CMV strains. The basic technique involves extraction of RNA from tomato leaf samples and then copied, while incorporating either fluorescent nucleotides or a tag that is later stained with fluorescence. Labeled RNA is then hybridized to a microarray for a period of time, then excess is washed off and the microarray is scanned under laser light. Different expression responses were resulted due to the type of viral infection.Total number of expressed genes were 3213, Out of this 1660 genes were down‐regulated and 1553 were up‐regulated. The response to CMV‐16 infection led to 1365 gene expression, 642 were down‐regulated and 723 genes were up‐regulated Specific seven different genes in tomato genome (Hsp70,ChMDH, Wif1, rccr, AAP2, PIIF & GAPDH endogenous gene used as a control) were analyzed and resulted in down regulation of Hsp70 and upper regulation of both ChMDH and PIIF. Gene expression results were confirmed with relative quantitative RT‐PCR technology.

Molecular cloning and characterisation of SlAGOfamily in tomato

BackgroundAGO (Argonaute) protein participates in plant developmental processes and virus defense as a core element of transcriptional regulator or/and post-transcriptional regulator in RNA induced silencing complex (RISC), which is guided by small RNAs to repress target genes expression. Previously, it was revealed that 15 putative AGO genes in tomato genome.ResultsIn present study, out of 15 detected SlAGO genes, only SlAGO4C and SlAGO15 couldn’t be detected in roots, stems, leaves, buds, flowers and fruit of tomato by 30 cycles of PCR. SlAGO7 could be detected in early stage of fruit (-2 dpa, 0 dpa and 4 dpa), but it was significantly down-regulated in fruit collected on the 6 days post anthesis. Moreover, SlAGO5 could only be detected in reproductive tissues and SlAGO4D was specifically detected in fruit. According to blast result with miRNA database, three SlAGO genes harbored complementary sequences to miR168 (SlAGO1A and SlAGO1B) or miR403 (SlAGO2A). 5′ RACE (Rapid amplification of cDNA ends) mapping was used to detect the 3′ cleavage products of SlAGO mRNAs. In addition, subcellular localization of SlAGO proteins was detected. Our results showed that most SlAGO proteins localized to nucleus and cytoplasm. Importantly, nuclear membrane localization of AGO proteins was observed. Furthermore, mutated miR168 complementary site of SlAGO1A resulted in expanded localization of SlAGO1A, indicating that miR168 regulated localization of SlAGO1A.ConclusionsOur results contribute to demonstration of potential roles of these newly isolated AGO family in tomato developmental processes and proved the conserved relationships between AGO genes and miRNAs in tomato, which might play important roles in tomato development and virus defense.

Superfamily of ankyrin repeat proteins in tomato

The ankyrin repeat (ANK) protein family plays a crucial role in plant growth and development and in response to biotic and abiotic stresses. However, no detailed information concerning this family is available for tomato (Solanum lycopersicum) due to the limited information on whole genome sequences. In this study, we identified a total of 130 ANK genes in tomato genome (SlANK), and these genes were distributed across all 12 chromosomes at various densities. And chromosomal localizations of SlANK genes indicated 25 SlANK genes were involved in tandem duplications. Based on their domain composition, all of the SlANK proteins were grouped into 13 subgroups. A combined phylogenetic tree was constructed with the aligned SlANK protein sequences. This tree revealed that the SlANK proteins comprise five major groups. An analysis of the expression profiles of SlANK genes in tomato in different tissues and in response to stresses showed that the SlANK proteins play roles in plant growth, development and stress responses. To our knowledge, this is the first report of a genome-wide analysis of the tomato ANK gene family. This study provides valuable information regarding the classification and putative functions of SlANK genes in tomato.

EXPRESSION PATTERNS OF AN ABIOTIC STRESS-INDUCIBLE DEHYDRATION RESPONSIVE ELEMENT BINDING PROTEIN-2 (DREB2) GENE IN TOMATO

A novel DREB (dehydration-responsive element binding) gene, designated as LeDREB2, was isolated from tomato. Based on multiple sequence alignment and phylogenetic characterization, LeDREB2 gene was classified into an A-2 group member of the DREBs family. We examined the expression pattern of LeDREB2 gene in tomato under different abiotic stresses. Southern blot analysis showed that LeDREB2 is a single copy gene in tomato genome. The organ specific expression profiling indicated that LeDREB2 gene was strongly expressed in young leaves and roots but weak expression in mature leaves and shoots. Northern blot analysis revealed that various kinds of environmental stress such as salt, drought and cold were significantly induced by LeDREB2 gene after application of time courses treatments except little increase in ABA. Our findings showed that the expression of LeDREB2 gene was induced by high salinity, drought and cold but not by the abscisic acid (ABA) treatment. These results indicated that the LeDREB2 gene is a member of the DREB transcription factors, which may play a role in both abiotic and oxidative stress responses.DOI: http://dx.doi.org/10.3329/bjpbg.v25i1.17006

Overaccumulation of Higher Polyamines in Ripening Transgenic Tomato Fruit Revives Metabolic Memory, Upregulates Anabolism-Related Genes, and Positively Impacts Nutritional Quality

Vegetables and fruits are essential components of the human diet as they are sources of vitamins, minerals, and fiber and provide antioxidants that prevent chronic diseases. Our goal is to improve durable nutritional quality of tomato fruit. We developed transgenic tomatoes expressing yeast S-adenosylmethionine decarboxylase (ySAMdc) gene driven by a fruit-specific E8 promoter to investigate the role of polyamines in fruit metabolism. Stable integration of E8-ySAMdc chimeric gene in tomato genome led to ripening-specific accumulation of polyamines, spermidine (Spd) and spermine (Spm), which in turn affected higher accumulation of glutamine, asparagine, and organic acids in the red fruit with significant decrease in the contents of valine, aspartate, sucrose, and glucose. The metabolite profiling analysis suggests that Spd/Spm are perceived as "signaling" organic-N metabolites by the fruit cells, resulting in the stimulation of carbon sequestration; enhanced synthesis of biomolecules; increased acid to sugar ratio, a good attribute for the fruit flavor; and in the accumulation of another "vital amine," choline, which is an essential micronutrient for brain development. A limited transcriptome analysis of the transgenic fruit that accumulate higher polyamines revealed a large number of differentially expressed genes, about 55% of which represented discrete functional categories, and the remaining 45% were novel, unknown, or unclassified: amino acid biosynthesis, carotenoid biosynthesis, cell wall metabolism, chaperone family, flavonoid biosynthesis, fruit ripening, isoprenoid biosynthesis, polyamine biosynthesis, signal transduction, stress/defense-related, transcription, translation, and vacuolar function. There was a good correspondence between some gene transcripts and their protein products, but not in the case of the tonoplast intrinsic protein, which showed post-transcriptional regulation. Higher metabolic activity of the transgenic fruit is reflected in higher respiratory activity, and upregulation of chaperones and mitochondrial cytochrome oxidase transcripts compared to the control. These transgenic plants are a new resource to understand the role of Spd/Spm in fruit biology. Transcriptome analysis and metabolic profiles of Spd/Spm accumulating, transgenic fruit suggest the presence of an intricate regulation and interconnection between certain metabolic pathways that are revived when Spd and Spm likely reach a certain threshold. Thus, polyamines act as antiapoptotic regulatory molecules and are able to revive metabolic memory in the tomato fruit.