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Tomato Solanum lycopersicum L. However, abiotic and biotic stresses severely hinder growth and development of the plant, which affects the production and quality of the crop. To reveal the potential roles of SOD genes under various stresses, we performed a systematic analysis of the tomato SOD gene family and analyzed the expression patterns of SlSOD genes in response to abiotic stresses at the whole-genome level. The characteristics of the SlSOD gene family were determined by analyzing gene structure, conserved motifs, chromosomal distribution, phylogenetic relationships, and expression patterns.
Phylogenetic analyses of SOD genes from tomato and other plant species were separated into two groups with a high bootstrap value, indicating that these SOD genes were present before the monocot-dicot split. Additionally, many cis-elements that respond to different stresses were found in the promoters of nine SlSOD genes. Microarray data analysis showed that most members of the SlSOD gene family were altered under salt- and drought-stress conditions.
This genome-wide analysis of SlSOD genes helps to clarify the function of SlSOD genes under different stress conditions and provides information to aid in further understanding the evolutionary relationships of SOD genes in plants.
Introduction It is well known that toxic free radicals caused by environmental stresses such as cold, drought, and water-logging are great challenges for crop production Mittler and Blumwald, Among them are reactive oxygen species ROStoxic free radicals produced in plant cells in response to stress, which can damage membranes, oxidize proteins, and cause DNA lesions Sun et al. However, in the process of evolution, plants have developed defense mechanisms to alleviate the damage caused by adverse environmental conditions.
Superoxide dismutases, a group of metalloenzymes, were first found in bovine erythrocytes in Mann and Keilin Subsequently, they were also described in bacteria, higher plants, and vertebrates Rabinowitch and Sklan, ; Tepperman and Dunsmuir, ; Kim et al. In plants, SODs have been detected in roots, leaves, fruits, and seeds Giannopolitis and Ries, ; Tepperman and Dunsmuir,where they provide basic protection to cells against oxidative stress.
FeSODs have been found in plant chloroplasts and cytoplasm Moran et al. MnSODs, widely present in all major kingdoms, have been observed in eukaryotic mitochondria Lynch and Kuramitsu, and can protect mitochondria by scavenging ROS Moller, In recent years, some studies have reported that SODs can protect plants against abiotic and biotic stresses, such as heat, cold, drought, salinity, abscisic acid and ethylene Wang et al. Under various environmental stress conditions, researchers have found that different types of SOD genes have different expression patterns.
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Moreover, SODs with the same metal cofactor did not always play the same role in different species. These results show that different SOD genes have different expression patterns in plants in response to diverse environmental stresses. Additionally, researchers have also found that alternative splicing and miRNAs may participate in the regulation of SOD expression Srivastava et al. To date, the SOD gene family has been described in many plant species, including Arabidopsis thaliana, Musa acuminata, Sorghum bicolor, and Populus trichocarpa Kliebenstein and Last, ; Molina-Rueda et al.
Tomato is not only an important staple and economic crop, but also plays a vital role as an experimental model plant Mueller et al. Further, Perl et al. Recently, great efforts have been made to explore the roles of SOD genes in improving tomato tolerance to various environmental stresses, such as heat, salt, drought, cold, and bacteria Mazorra et al.
In addition, several recent studies have indicated that SOD played an important role of hormone and insecticide stresses. For example, Bernal et al. As described above, SOD gene families have been widely implicated in responses to abiotic and biotic stresses in tomato. However, these studies have mainly concentrated on the expression of a single form of SOD enzyme and on changes in the enzymatic antioxidant system under various environmental stresses, and little has been reported on the SOD gene family in tomato.
To comprehensively understand the putative roles of SOD genes in tomato, a systematic analysis of the SOD gene family was necessary at the whole-genome level.
Recently, the whole-genome sequence of tomato was made available, which provided opportunities for analyzing the expression patterns and regulation mechanisms of the tomato SOD SlSOD gene family in response to environment stresses.
Hence, the objectives of this study were i to identify the SOD gene family in tomato; ii to analyze gene structure, duplication and expression patterns in different tomato tissues; iii to illustrate chromosomal locations and phylogenetic relationships with SODs from other plants; and iv to reveal the regulating mechanisms of the SlSOD gene family under abiotic salt and drought stress by using real-time fluorescence quantitative PCR qRT-PCR.
First, the whole tomato genome was downloaded from Sol Genomics Network SGN 1 and a local database was constructed using the software Bioedit 7.
For BlastP, e-value was set at 1e All redundant putative SOD sequences were excluded. Physicochemical characteristics of SOD amino acid sequences were predicted by the Protparam tool 3including molecular weight MWand theoretical isoelectric point pI Gasteiger et al. In addition, to reveal the evolutionary relationships between SOD genes in different plant species, potential SOD genes from eight plant species were selected for phylogenetic analysis.
Among them, SOD genes from four plant species Vitis vinifera, Solanum tuberosum, Zea mays, and Panicum miliaceum were identified using the same method above. The SOD genes of the remaining plant species Poplar, Arabidopsis thaliana, Oryza sativa, Sorghum bicolor were derived from previously published studies Kliebenstein and Last, ; Dehury et al.
We used the method described by Feng et al. Tandemly duplicated SlSOD genes were identified according to methods reported by previous researchers Yang and Tuskan, ; Tuskan et al. A phylogenetic tree was constructed using the software MEGA5.
In the phylogenetic tree, the degree of support for a particular grouping pattern was evaluated using bootstrap replicates value Filiz et al.
The tree was viewed with FigTree v1. Ten different tissues were selected: Plant Materials and Stress Treatment Seeds of a tomato breeding strain, Zhe fenwere germinated on water-saturated filter paper. Then, seeds were washed three times with distilled water. Three biological replications were carried out.
Before reverse transcription, the quality of RNA samples was checked by agarose gel electrophoresis.
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- Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq
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The quality and specificity of primers was determined by the melt curve Feng et al. Three independent technical replicates were performed for each of the SlSOD genes. The length ranged from to AA, MW ranged from The remaining members were localized in the chloroplast.Grafting a Tomato to a Potato
The characteristics of SOD genes from Solanum lycopersicum. Eight different motifs commonly observed in tomato protein sequences by MEME server. Conserved motif analysis of SlSOD proteins.
Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq
Reannotation included the splitting of gene models, combination of partial genes to a longer sequence and closing of assembly gaps. Within the draft S. Phylogenetic analyses show a high conservation of all NB-LRR classes between HeinzLA and the potato clone DM, suggesting that all sub-families were already present in the last common ancestor.
Use of RenSeq on cDNA from uninfected and late blight-infected tomato leaves allows the avoidance of sequence analysis of non-expressed paralogues. Conclusion RenSeq is a promising method to facilitate analysis of plant resistance gene complements.
The reannotated tomato NB-LRR complements, phylogenetic relationships and chromosomal locations provided in this paper will provide breeders and scientists with a useful tool to identify novel disease resistance traits. Defence activation requires pathogen detection, which can occur outside or inside the plant cell, by one of two known distinct recognition mechanisms [ 2 - 4 ].
The first line of detection resides at the cell surface and involves recognition of pathogen-associated molecular patterns PAMPs through cell surface transmembrane receptors.
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Plants in turn possess a second line of defence, which is represented by proteins that detect specific effector molecules or their effects on host cell components. These intracellular immune receptors, termed R resistance genes, encode proteins that resemble mammal NOD-like receptors and typically carry a nucleotide binding and leucine-rich repeat domains NB-LRR.
The non-TIR class CNLs is less well defined, but some members of this class contain helical coiled-coil—like CC sequences in their amino-terminal domain [ 1 ].
Tomato is the second most important vegetable crop worldwide faostat. Several NB-LRR type R genes have been cloned from tomato, potato and pepper, and are used in current breeding efforts. The first draft tomato genome assembly revealed the large size of the NB-LRR gene family, and thus the potential R gene repertoire [ 7 ].