Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World

Unlike other important Solanaceae crops such as tomato, potato, chili pepper, and tobacco, all of which originated in South America and are cultivated worldwide, eggplant (Solanum melongena L.) is indigenous to the Old World and in this respect it is phylogenetically unique. To broaden our knowledge of the genomic nature of solanaceous plants further, we dissected the eggplant genome and built a draft genome dataset with 33,873 scaffolds termed SME_r2.5.1 that covers 833.1 Mb, ca. 74% of the eggplant genome. Approximately 90% of the gene space was estimated to be covered by SME_r2.5.1 and 85,446 genes were predicted in the genome. Clustering analysis of the predicted genes of eggplant along with the genes of three other solanaceous plants as well as Arabidopsis thaliana revealed that, of the 35,000 clusters generated, 4,018 were exclusively composed of eggplant genes that would perhaps confer eggplant-specific traits. Between eggplant and tomato, 16,573 pairs of genes were deduced to be orthologous, and 9,489 eggplant scaffolds could be mapped onto the tomato genome. Furthermore, 56 conserved synteny blocks were identified between the two species. The detailed comparative analysis of the eggplant and tomato genomes will facilitate our understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.     

In silico prediction of proteins related to xyloglucan fucosyltransferases in Solanaceae genomes

Two independent studies have shown that the cell wall of pollen tubes from tobacco and tomato species contained fucosylated xyloglucan (XyG). These findings are intriguing as many reports have shown that XyG of somatic cells of these species is not fucosylated but instead is arabinosylated. In order to produce fucosylated XyG, plants must express a functional galactoside α-2-fucosyltransferase. Here, using a bioinformatics approach, we show that several candidate genes coding for XyG fucosyltransferases are present in the genome of coffee and several Solanaceae species including tomato, tobacco, potato, eggplant and pepper. BLAST and protein alignments with the 2 well-characterized XyG fucosyltransferases from Arabidopsis thaliana and Pisum sativum revealed that at least 6 proteins from different Solanaceae species and from coffee displayed the 3 conserved motifs required for XyG fucosyltransferase activity.     

Comparative genome analysis of pathogenic and non-pathogenic Clavibacter strains reveals adaptations to their lifestyle

Background

The genus Clavibacter harbors economically important plant pathogens infecting agricultural crops such as potato and tomato. Although the vast majority of Clavibacter strains are pathogenic, there is an increasing number of non-pathogenic isolates reported. Non-pathogenic Clavibacter strains isolated from tomato seeds are particularly problematic because they affect the current detection and identification tests for Clavibacter michiganensis subsp. michiganensis (Cmm), which is regulated with a zero tolerance in tomato seed. Their misidentification as pathogenic Cmm hampers a clear judgment on the seed quality and health.

Results

To get more insight in the genetic features linked to the lifestyle of these bacteria, a whole-genome sequence of the tomato seed-borne non-pathogenic Clavibacter LMG 26808 was determined. To gain a better understanding of the molecular determinants of pathogenicity, the genome sequence of LMG 26808 was compared with that of the pathogenic Cmm strain (NCPPB 382). The comparative analysis revealed that LMG 26808 does not contain plasmids pCM1 and pCM2 and also lacks the majority of important virulence factors described so far for pathogenic Cmm. This explains its apparent non-pathogenic nature in tomato plants. Moreover, the genome analysis of LMG 26808 detected sequences from a plasmid originating from a member of Enterobacteriaceae/Klebsiella relative. Genes received that way and coding for antibiotic resistance may provide a competitive advantage for survival of LMG 26808 in its ecological niche. Genetically, LMG 26808 was the most similar to the pathogenic Cmm NCPPB 382 but contained more mobile genetic elements. The genome of this non-pathogenic Clavibacter strain contained also a high number of transporters and regulatory genes.

Conclusions

The genome sequence of the non-pathogenic Clavibacter strain LMG 26808 and the comparative analyses with other pathogenic Clavibacter strains provided a better understanding of the genetic bases of virulence and adaptation mechanisms present in the genus Clavibacter.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-392) contains supplementary material, which is available to authorized users.     

The AOC promoter of tomato is regulated by developmental and environmental stimuli

The allene oxide cyclase (AOC) catalyzes the formation of cis-(+)-12-oxophytodienoic acid, an intermediate in jasmonate biosynthesis and is encoded by a single copy gene in tomato. The full length AOC promoter isolated by genome walk contains 3600 bp. Transgenic tomato lines carrying a 1000 bp promoter fragment and the full length promoter, respectively, in front of the beta-glucuronidase (GUS)-encoding uidA gene and several tobacco lines carrying the full length tomato AOC promoter before GUS were used to record organ- and tissue-specific promoter activities during development and in response to various stimuli. High promoter activities corresponding to immunocytochemically detected occurrence of the AOC protein were found in seeds and young seedlings and were confined to the root tip, hypocotyl and cotyledons of 3-d-old seedlings. In 10-d-old seedlings promoter activity appeared preferentially in the elongation zone. Fully developed tomato leaves were free of AOC promoter activity, but showed high activity upon wounding locally and systemically or upon treatment with JA, systemin or glucose. Tomato flowers showed high AOC promoter activities in ovules, sepals, anthers and pollen. Most of the promoter activity patterns found in tomato with the 1000 bp promoter fragment were also detected with the full length tomato AOC promoter in tobacco during development or in response to various stimuli. The data support a spatial and temporal regulation of JA biosynthesis during development and in response to environmental stimuli.     

Genome-wide identification of cytosine-5 DNA methyltransferases and demethylases in Solanum lycopersicum

Recent studies have reported that decreased level of DNA cytosine methylation in the global genome was closely related to the initiation of tomato (Solanum lycopersicum) fruit ripening. However, genome-scale analysis of cytosine-5 DNA methyltransferases (C5-MTases) and demethylases in tomato has not been engaged. In this study, 7 C5-MTases and 3 demethylases were identified in tomato genome, which probably contributed to DNA cytosine methylation level in tomato. The 7 C5-MTases were categorized into 4 subgroups, and the 3 demethylases were classified into 2 subgroups based on phylogenetic analyses. Comprehensive analysis of their structure and genomic localization was also performed in this paper. According to online RNA-seq data, 4 S. lycopersicum C5-MTase (SlC5-MTase) genes (SlMET, SlDRM1L1, SlDRM5, SlMET3L) were expressed higher than others, and one DNA demethylase gene (SlDML) was significantly changed during tomato fruit development and ripening. Furthermore, all these five gene expressions at breaker (BK) stage changed with 1-methylcyclopropene (1-MCP) treatment, indicating that they were regulated by ethylene directly or indirectly in tomato fruit. In addition, subcellular localization analysis indicated that SlDRM1L1 and SlDRM5 located in the nucleus might have responsibility for RNA-directed DNA methylation (RdDM). Collectively, this paper provided a framework for gene discovery and functional characterization of C5-MTases and DNA demethylases in other Solanaceae species.     

Editor's choice: Genome-Wide SNP Genotyping to Infer the Effects on Gene Functions in Tomato

The genotype data of 7054 single nucleotide polymorphism (SNP) loci in 40 tomato lines, including inbred lines, F₁ hybrids, and wild relatives, were collected using Illumina''s Infinium and GoldenGate assay platforms, the latter of which was utilized in our previous study. The dendrogram based on the genotype data corresponded well to the breeding types of tomato and wild relatives. The SNPs were classified into six categories according to their positions in the genes predicted on the tomato genome sequence. The genes with SNPs were annotated by homology searches against the nucleotide and protein databases, as well as by domain searches, and they were classified into the functional categories defined by the NCBI''s eukaryotic orthologous groups (KOG). To infer the SNPs'' effects on the gene functions, the three-dimensional structures of the 843 proteins that were encoded by the genes with SNPs causing missense mutations were constructed by homology modelling, and 200 of these proteins were considered to carry non-synonymous amino acid substitutions in the predicted functional sites. The SNP information obtained in this study is available at the Kazusa Tomato Genomics Database (http://plant1.kazusa.or.jp/tomato/).     

Molecular Transfer of Nematode Resistance Genes

Recombinant DNA techniques have been used to introduce agronomically valuable traits, including resistance to viruses, herbicides, and insects, into crop plants. Introduction of these genes into plants frequently involves Agrobacterium-mediated gene transfer. The potential exists for applying this technology to nematode control by introducing genes conferring resistance to nematodes. Transferred genes could include those encoding products detrimental to nematode development or reproduction as well as cloned host resistance genes. Host genes that confer resistance to cyst or root-knot nematode species have been identified in many plants. The best characterized is Mi, a gene that confers resistance to root-knot nematodes in tomato. A map-based cloning approach is being used to isolate the gene. For development of a detailed map of the region of the genome surrounding Mi, DNA markers genetically linked to Mi have been identified and analyzed in tomato lines that have undergone a recombination event near Mi. The molecular map will be used to identify DNA corresponding to Mi. We estimate that a clone of Mi will be obtained in 2-5 years. An exciting prospect is that introduction of this gene will confer resistance in plant species without currently available sources of resistance.     

Effect of Soils from Six Management Systems on Root-knot Nematodes and Plant Growth in Greenhouse Assays

The effects of soil management systems on root-knot nematode (Meloidogyne incognita) eggs and gall incidence on tomato (Lycopersicon esculentum) and cucumber (Cucumis sativus) following tomato were evaluated. Soil was collected from a replicated field experiment in which six management systems were being assessed for vegetable production. Soil management systems were conventional production, organic production, bahiagrass (Paspalum notatum) pasture, bahiagrass: Stylosanthes (Stylosanthes guianensis) pasture, bare ground fallow, and weed fallow. Soil was collected from field plots and used in greenhouse experiments. Identification of egg-parasitic fungi and the incidence of root-knot nematode galling were assessed both on tomato and cucumber planted in the same pots following the removal of tomato plants. Organic, bare ground fallow and conventional production treatments reduced galling both on tomato and on cucumber following tomato. Although no treatment consistently enhanced egg-parasitic fungi, management system did affect egg viability and the types of fungi isolated from parasitized eggs.     

Reproduction of Virulent Isolates of Meloidogyne incognita on Susceptible and Mi-resistant Tomato

The reproductive potential of natural and laboratory-selected Meloidogyne incognita isolates virulent against the tomato Mi resistance gene, all derived from a single egg-mass, were compared when the nematodes were inoculated on susceptible and resistant tomato. Fewer second-stage juveniles (P = 0.01) of the two virulent populations selected under laboratory conditions matured to females on the resistant tomato compared to the susceptible cultivar. In contrast, no differences were found between the number of egg masses produced on the resistant versus the susceptible tomato by the two natural virulent isolates. No clear general trends concerning the fecundity of the females could be inferred from the comparative analysis of the numbers of eggs per egg mass x tomato cultivar combination. These observations suggested that the genetic changes induced under environmentally controlled nematode growth might be different from those occurring in natural Mi-resistance breaking biotypes grown without environmental control.     

Trap Crops and Population Management of Globodera tabacum tabacum

Tobacco, eastern black nightshade, and tomato were grown for 3 to 13 weeks to assess differences in invasion, development, and soil density of Globodera tabacum tabacum (tobacco cyst nematode) in field plots and microplots over three seasons. Tobacco cyst nematodes invaded roots of resistant and susceptible tobacco, nightshade, and tomato. Nematode development was fastest in nightshade and slowest in tomato, and few adults developed in roots of nematode-resistant tobacco. Soil populations of tobacco cyst nematodes were reduced up to 80% by destroying nightshade or susceptible tobacco grown for 3 to 6 weeks. Nematode populations were reduced up to 96% by destroying tomato or resistant tobacco grown for 3 to 6 weeks. Timing of crop destruction was less critical with tomato and resistant tobacco, as nematode populations did not increase after 13 weeks of growth. These studies demonstrate that trap cropping, through crop destruction, can significantly reduce G. t. tabacum populations.     

Managing Nematode Population Densities on Tomato Transplants Using Crop Rotation and a Nematicide

Millet, milo, soybean, crotalaria, and Norman pigeon pea were used in conjunction with clean fallow and a nematicide (fensulfothion) for managing nematode populations in the production of tomato transplants (Lycopersicon esculentum Mill.). Glean fallow was the most effective treatment in suppressing nematode numbers. After 2 years in tomato, root-knot nematodes increased in numbers to damaging levels, and fallow was no longer effective for complete control even in conjunction with fensulfothion. After 4 years in tomato, none of the crops used as summer cover crops alone or in conjunction with fensulfothion reduced numbers of root-knot nematodes in harvested tomato transplants sufficiently to meet Georgia certification regulations. Milo supported large numbers of Macroposthonia ornata and Pratylenchus spp. and crotalaria supported large numbers of Pratylenchus spp. Millet, milo, soybean, crotalaria, and pigeon pea are poor choices for summer cover crops in sites used to produce tomato transplants, because they support large populations of root-knot and other potentially destructive nematodes.     

Control of Root-knot Nematodes on Tomato in Stone Wool Substrate with Biological Nematicides

The efficacy of four biological nematicides on root-galling, root-knot nematode (Meloidogyne incognita) reproduction, and shoot weight of tomato (Solanum lycopersicum) grown in stone wool substrate or in pots with sandy soil was compared to an oxamyl treatment and a non-treated control. In stone wool grown tomato, Avid® (a.i. abamectin) was highly effective when applied as a drench at time of nematode inoculation. It strongly reduced root-galling and nematode reproduction, and prevented a reduction in tomato shoot weight. However, applying the product one week before, or two weeks after nematode inoculation was largely ineffective. This shows that Avid® has short-lived, non-systemic activity. The effects of Avid® on nematode symptoms and reproduction on soil-grown tomato were only very minor, probably due to the known strong adsorption of the active ingredient abamectin to soil particles. The neem derived product Ornazin® strongly reduced tomato root-galling and nematode reproduction only in stone wool and only when applied as a drench one week prior to nematode inoculation, suggesting a local systemic activity or modification of the root system, rendering them less suitable host for the nematodes. This application however also had some phytotoxic effect, reducing tomato shoot weights. The other two products, Nema-Q™ and DiTera®, did not result in strong or consistent effects on nematode symptoms or reproduction.     

The Potential of Five Winter-grown Crops to Reduce Root-knot Nematode Damage and Increase Yield of Tomato

Broccoli (Brassica oleracea), carrot (Daucus carota), marigold (Tagetes patula), nematode-resistant tomato (Solanum lycopersicum), and strawberry (Fragaria ananassa) were grown for three years during the winter in a root-knot nematode (Meloidogyne incognita) infested field in Southern California. Each year in the spring, the tops of all crops were shredded and incorporated in the soil. Amendment with poultry litter was included as a sub-treatment. The soil was then covered with clear plastic for six weeks and M. incognita-susceptible tomato was grown during the summer season. Plastic tarping raised the average soil temperature at 13 cm depth by 7°C.The different winter-grown crops or the poultry litter did not affect M. incognita soil population levels. However, root galling on summer tomato was reduced by 36%, and tomato yields increased by 19% after incorporating broccoli compared to the fallow control. This crop also produced the highest amount of biomass of the five winter-grown crops. Over the three-year trial period, poultry litter increased tomato yields, but did not affect root galling caused by M. incognita. We conclude that cultivation followed by soil incorporation of broccoli reduced M. incognita damage to tomato. This effect is possibly due to delaying or preventing a portion of the nematodes to reach the host roots. We also observed that M. incognita populations did not increase under a host crop during the cool season when soil temperatures remained low (< 18°C).     

Pathological Interaction of a Combination of Heterodera schachtii and Meloidogyne hapla on Tomato

Increased culturing of a tomato population of Heterodera schachtii (UT1C) on tomato for 480 days (eight inoculation periods of 60 days each) significantly increased virulence to ''Stone Improved'' tomato. A synergistic relationship existed between Meloidogyne hapla and H. schaehtii on tomato. A combination of H. schachtii (UTIC) and M. hapla significantly reduced tomato root weights by 65, 64, and 61% below root weights of untreated controls, and single inoculations of M. hapla and H. schachtii, respectively. This corresponded to root reductions of 42, 44, and 46% from a combination of H. schachtii (UT1B) and M. hapla. Antagonism existed between H. schachtii and M. hapla with regard to infection courts and feeding sites. The root-knot galling index dropped from 6.0 with a single inoculation of M. hapla to 4.3 and 3.3 with combined inoculations of M. hapla plus UT1B and M. hapla plus UTIC cyst nematode populations. The pathological virulence of H. schachtii to sugarbeet was not lost by extended culturing on tomato; there were no differences in penetration, maturation, and reproduction between sugarbeet populations continually cultured on sugarbeet and the population continually cultured on tomato.     

SNP Discovery and Linkage Map Construction in Cultivated Tomato

Few intraspecific genetic linkage maps have been reported for cultivated tomato, mainly because genetic diversity within Solanum lycopersicum is much less than that between tomato species. Single nucleotide polymorphisms (SNPs), the most abundant source of genomic variation, are the most promising source of polymorphisms for the construction of linkage maps for closely related intraspecific lines. In this study, we developed SNP markers based on expressed sequence tags for the construction of intraspecific linkage maps in tomato. Out of the 5607 SNP positions detected through in silico analysis, 1536 were selected for high-throughput genotyping of two mapping populations derived from crosses between ‘Micro-Tom’ and either ‘Ailsa Craig’ or ‘M82’. A total of 1137 markers, including 793 out of the 1338 successfully genotyped SNPs, along with 344 simple sequence repeat and intronic polymorphism markers, were mapped onto two linkage maps, which covered 1467.8 and 1422.7 cM, respectively. The SNP markers developed were then screened against cultivated tomato lines in order to estimate the transferability of these SNPs to other breeding materials. The molecular markers and linkage maps represent a milestone in the genomics and genetics, and are the first step toward molecular breeding of cultivated tomato. Information on the DNA markers, linkage maps, and SNP genotypes for these tomato lines is available at http://www.kazusa.or.jp/tomato/.     

Potential of Foliar,Dip, and Injection Applications of Avermectins for Control of Plant-Parasitic Nematodes

Studies were conducted to determine the potential of two avermectin compounds, abamectin and emamectin benzoate, for controlling plant-parasitic nematodes when applied by three methods: foliar spray, root dip, and pseudostem injection. Experiments were conducted against Meloidogyne incognita on tomato, M. javanica on banana, and Radopholus similis on banana. Foliar applications of both avermectins to banana and tomato were not effective for controlling any of the nematodes evaluated. Root dips of banana and tomato were moderately effective for controlling M. incognita on tomato and R. similis on banana. Injections (1 ml) of avermectins into banana pseudostems were effective for controlling M. javanica and R similis, and were comparable to control achieved with a conventional chemical nematicide, fenamiphos. Injections of 125 to 2,000 μg/plant effectively controlled one or both nematodes on banana; abamectin was more effective than emamectin benzoate for controlling nematodes.