Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments

Analysis of Heat Shock Proteins Based on Amino Acids for the Tomato Genome

This research aimed to investigate heat shock proteins in the tomato genome through the analysis of amino acids. The highest length among sequences was found in seq19 with 3534 base pairs. This seq19 was reported and contained a family of proteins known as HsfA that have a domain of transcriptional activation for tolerance to heat and other abiotic stresses. The values of the codon adaptation index (CAI) ranged from 0.80 in Seq19 to 0.65 in Seq10, based on the mRNA of heat shock proteins for tomatoes. Asparagine (AAT, AAC), aspartic acid (GAT, GAC), phenylalanine (TTT, TTC), and tyrosine (TAT, TAC) have relative synonymous codon usage (RSCU) values bigger than 0.5. In modified relative codon bias (MRCBS), the high gene expressions of the amino acids under heat stress were histidine, tryptophan, asparagine, aspartic acid, lysine, phenylalanine, isoleucine, cysteine, and threonine. RSCU values that were less than 0.5 were considered rare codons that affected the rate of translation, and thus selection could be effective by reducing the frequency of expressed genes under heat stress. The normal distribution of RSCU shows about 68% of the values drawn from the standard normal distribution were within 0.22 and -0.22 standard deviations that tend to cluster around the mean. The most critical component based on principal component analysis (PCA) was the RSCU. These findings would help plant breeders in the development of growth habits for tomatoes during breeding programs.

Insights into the Transcriptional Reprogramming in Tomato Response to PSTVd Variants Using Network Approaches

Viroids are the smallest pathogens of angiosperms, consisting of non-coding RNAs that cause severe diseases in agronomic crops. Symptoms associated with viroid infection are linked to developmental alterations due to genetic regulation. To understand the global mechanisms of host viroid response, we implemented network approaches to identify master transcription regulators and their differentially expressed targets in tomato infected with mild and severe variants of PSTVd. Our approach integrates root and leaf transcriptomic data, gene regulatory network analysis, and identification of affected biological processes. Our results reveal that specific bHLH, MYB, and ERF transcription factors regulate genes involved in molecular mechanisms underlying critical signaling pathways. Functional enrichment of regulons shows that bHLH-MTRs are linked to metabolism and plant defense, while MYB-MTRs are involved in signaling and hormone-related processes. Strikingly, a member of the bHLH-TF family has a specific potential role as a microprotein involved in the post-translational regulation of hormone signaling events. We found that ERF-MTRs are characteristic of severe symptoms, while ZNF-TF, tf3a-TF, BZIP-TFs, and NAC-TF act as unique MTRs. Altogether, our results lay a foundation for further research on the PSTVd and host genome interaction, providing evidence for identifying potential key genes that influence symptom development in tomato plants.

Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato

The tomato gray leaf spot resistance gene Sm was fine-mapped in a 185-kb region through a map-based cloning strategy and genome-wide association study; a candidate gene was proved to be involved in Sm-mediated resistance through transient gene silencing. Gray leaf spot, caused by Stemphylium spp., is a warm weather foliar disease in tomato (Solanum lycopersicum L). Resistance against gray leaf spot is conferred by a single incompletely dominant gene (Sm) located on chromosome 11. This study aimed to map and identify molecular marker tightly linked to the Sm gene for the use of marker-assisted selection in breeding. Using an F₂ population derived from a cross between the resistant line '9706' and the susceptible line 'Heinz 1706', the Sm gene was mapped to a 185-kb interval between two markers, InDel343 and InDel-FT-32 on chromosome 11, which was consistent with the result of a genome-wide association study using 289 diverse accessions. An ORF predicted in this region was proved to be involved in Sm-mediated resistance through transient gene silencing and seems to be a good candidate of the Sm locus. To clone the Sm gene, a bacterial artificial chromosome (BAC) library was screened and one BAC clone B80B15 containing the predicted ORF was identified. The analysis of sequence and structure characteristics demonstrated that the candidate gene was not a typical type resistance gene. Additionally, a co-dominant marker Sm-InDel, which produced a 122-bp or 140-bp fragment for resistant or susceptible alleles, respectively, was developed. This marker was validated in 289 germplasm and could be used in marker-assisted selection for gray leaf spot resistance.

Genome-wide analysis of the NAC transcription factor family in Tartary buckwheat (Fagopyrum tataricum)

BACKGROUND

The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, there is no comprehensive study on the NAC genes of Tartary buckwheat (Fagopyrum tataricum), a large group of extensively cultivated medicinal and edible plants. The recently published Tartary buckwheat genome permits us to explore all the FtNAC genes on a genome-wide basis.

RESULTS

In the present study, 80 NAC (FtNAC) genes of Tartary buckwheat were obtained and named uniformly according to their distribution on chromosomes. Phylogenetic analysis of NAC proteins in both Tartary buckwheat and Arabidopsis showed that the FtNAC proteins are widely distributed in 15 subgroups with one subgroup unclassified. Gene structure analysis found that multitudinous FtNAC genes contained three exons, indicating that the structural diversity in Tartary buckwheat NAC genes is relatively low. Some duplication genes of FtNAC have a conserved structure that was different from others, indicating that these genes may have a variety of functions. By observing gene expression, we found that FtNAC genes showed abundant differences in expression levels in various tissues and at different stages of fruit development.

CONCLUSIONS

In this research, 80 NAC genes were identified in Tartary buckwheat, and their phylogenetic relationships, gene structures, duplication, global expression and potential roles in Tartary buckwheat development were studied. Comprehensive analysis will be useful for a follow-up study of functional characteristics of FtNAC genes and for the development of high-quality Tartary buckwheat varieties.

Transcriptome Analysis of the Cf-12-Mediated Resistance Response to Cladosporium fulvum in Tomato

Cf-12 is an effective gene for resisting tomato leaf mold disease caused by Cladosporium fulvum (C. fulvum). Unlike many other Cf genes such as Cf-2, Cf-4, Cf-5, and Cf-9, no physiological races of C. fulvum that are virulent to Cf-12 carrying plant lines have been identified. In order to better understand the molecular mechanism of Cf-12 gene resistance response, RNA-Seq was used to analyze the transcriptome changes at three different stages of C. fulvum infection (0, 4, and 8 days post infection [dpi]). A total of 9100 differentially expressed genes (DEGs) between 4 and 0 dpi, 8643 DEGs between 8 and 0 dpi and 2547 DEGs between 8 and 4 dpi were identified. In addition, we found that 736 DEGs shared among the above three groups, suggesting the presence of a common core of DEGs in response to C. fulvum infection. These DEGs were significantly enriched in defense-signaling pathways such as the calcium dependent protein kinases pathway and the jasmonic acid signaling pathway. Additionally, we found that many transcription factor genes were among the DEGs, indicating that transcription factors play an important role in C. fulvum defense response. Our study provides new insight on the molecular mechanism of Cf resistance to C. fulvum, especially the unique features of Cf-12 in responding to C. fulvum infection.

Tracing the evolution of the floral homeotic B- and C-function genes through genome synteny

The evolution of the floral homeotic genes has been characterized using phylogenetic and functional studies. It is possible to enhance these studies by comparing gene content and order between species to determine the evolutionary history of the regulatory genes. Here, we use a synteny-based approach to trace the evolution of the floral B- and C-function genes that are required for specification of the reproductive organs. Consistent with previous phylogenetic studies, we show that the euAP3-TM6 split occurred after the monocots and dicots diverged. The Arabidopsis TM6 and papaya euAP3 genes are absent from the respective genomes, and we have detected loci from which these genes were lost. These data indicate that either the TM6 or the euAP3 lineage genes can be lost without detriment to flower development. In contrast, PI is essential for male reproductive organ development; yet, contrary to predictions, complex genomic rearrangements have resulted in almost complete breakdown of synteny at the PI locus. In addition to showing the evolution of B-function genes through the prediction of ancestral loci, similar reconstructions reveal the origins of the C-function AG and PLE lineages in dicots, and show the shared ancestry with the monocot C-function genes. During our studies, we found that transposable elements (TEs) present in sequenced Antirrhinum genomic clones limited comparative studies. A pilot survey of the Antirrhinum data revealed that gene-rich regions contain an unusually high degree of TEs of very varied types, which will be an important consideration for future genome sequencing efforts.

Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider

DNA sequences provide useful insights into genome structure and organization as well as evolution of species. We report on a detailed analysis of the locus surrounding the tomato (Solanum lycopersicum) fruit-shape gene SUN to determine the driving force and genome environment that foster the appearance of novel phenotypes. The gene density at the sun locus is similar to that described in other euchromatic portions of the tomato genome despite the relatively high number of transposable elements. Genes at the sun locus include protein-coding as well as RNA genes, are small in size, and belong to families that were duplicated at the locus an estimated 5-74 million years ago. In general, the DNA transposons at the sun locus are older than the RNA transposons, and their insertion pre-dates the speciation of S. lycopersicum and S. pimpinellifolium. Gene redundancy and large intergenic regions may explain the tolerance of the sun locus to frequent rearrangements and transpositions. The most recent transposition event at the sun locus involved Rider, a recently discovered high-copy retrotransposon. Rider probably arose early during the speciation of tomato. The element inserts into or near to genes and may still be active, which are unusual features for a high-copy element. Rider full-length and read-through transcripts past the typical transcription termination stop are detected, and the latter are required for mobilizing nearby sequences. Rider activity has resulted in an altered phenotype in three known cases, and may therefore have played an important role in tomato evolution and domestication.

Genome analysis and genetic enhancement of tomato

The Solanaceae is an important family of vegetable crops, ornamentals and medicinal plants. Tomato has served as a model member of this family largely because of its enriched cytogenetic, genetic, as well as physical, maps. Mapping has helped in cloning several genes of importance such as Pto, responsible for resistance against bacterial speck disease, Mi-1.2 for resistance against nematodes, and fw2.2 QTL for fruit weight. A high-throughput genome-sequencing program has been initiated by an international consortium of 10 countries. Since heterochromatin has been found to be concentrated near centromeres, the consortium is focusing on sequencing only the gene-rich euchromatic region. Genomes of the members of Solanaceae show a significant degree of synteny, suggesting that the tomato genome sequence would help in the cloning of genes for important traits from other Solanaceae members as well. ESTs from a large number of cDNA libraries have been sequenced, and microarray chips, in conjunction with wide array of ripening mutants, have contributed immensely to the understanding of the fruit-ripening phenomenon. Work on the analysis of the tomato proteome has also been initiated. Transgenic tomato plants with improved abiotic stress tolerance, disease resistance and insect resistance, have been developed. Attempts have also been made to develop tomato as a bioreactor for various pharmaceutical proteins. However, control of fruit quality and ripening remains an active and challenging area of research. Such efforts should pave the way to improve not only tomato, but also other solanaceous crops.

[Advances of gene enrichment in plant genome]

The genome size varies greatly in higher plants. Repetitive sequences account for most of the large plant genomes while low-copy or single copy genic sequences, referred to as gene space, take up only a small portion of the genomes. Considering the large amount of repetitive sequences, it is a great challenge to obtain genic sequences using high-throughout methods in non-model plants bearing large genomes. Currently, several approaches have been developed for gene enrichment on a genome-wide scale, such as cDNA library, methylation filtration library, high Cot library and transposon tagging. Here, we reviewed the technical principles, advantages and disadvantages of these methods, as well as the recent development of methylation filtration technology. An in-depth discussion was performed for selection of one method or combination of methods according to the research objectives and plant materials, especially for plants with large genomes.