Solanum torvum responses to the root-knot nematode Meloidogyne incognita

Abstract

BackgroundSolanum torvum Sw is worldwide employed as rootstock for eggplant cultivation because of its vigour and resistance/tolerance to the most serious soil-borne diseases as bacterial, fungal wilts and root-knot nematodes. The little information on Solanum torvum (hereafter Torvum) resistance mechanisms, is mostly attributable to the lack of genomic tools (e.g. dedicated microarray) as well as to the paucity of database information limiting high-throughput expression studies in Torvum.ResultsAs a first step towards transcriptome profiling of Torvum inoculated with the nematode M. incognita, we built a Torvum 3’ transcript catalogue. One-quarter of a 454 full run resulted in 205,591 quality-filtered reads. De novo assembly yielded 24,922 contigs and 11,875 singletons. Similarity searches of the S. torvum transcript tags catalogue produced 12,344 annotations. A 30,0000 features custom combimatrix chip was then designed and microarray hybridizations were conducted for both control and 14 dpi (day post inoculation) with Meloidogyne incognita-infected roots samples resulting in 390 differentially expressed genes (DEG). We also tested the chip with samples from the phylogenetically-related nematode-susceptible eggplant species Solanum melongena. An in-silico validation strategy was developed based on assessment of sequence similarity among Torvum probes and eggplant expressed sequences available in public repositories. GO term enrichment analyses with the 390 Torvum DEG revealed enhancement of several processes as chitin catabolism and sesquiterpenoids biosynthesis, while no GO term enrichment was found with eggplant DEG.The genes identified from S. torvum catalogue, bearing high similarity to known nematode resistance genes, were further investigated in view of their potential role in the nematode resistance mechanism.ConclusionsBy combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling in a non-model species. In addition, the development of an in silico validation strategy allowed to further extend the use of the custom chip to a related species and to assess by comparison the expression of selected genes without major concerns of artifacts. The expression profiling of S. torvum responses to nematode infection points to sesquiterpenoids and chitinases as major effectors of nematode resistance. The availability of the long sequence tags in S. torvum catalogue will allow precise identification of active nematocide/nematostatic compounds and associated enzymes posing the basis for exploitation of these resistance mechanisms in other species.

Comparative transcriptome analysis of eggplant (Solanum melongena L.) and turkey berry (Solanum torvum Sw.): phylogenomics and disease resistance analysis

“…Our assemblies were of substantially higher quality than those generated in previous studies [15, 16]. In a comparative analysis of eggplant ESTs [15], only 16,245 unigenes were constructed, which is less than half of our 34,174 unigenes and of the genes identified in the closely related potato (39,031) [1] and tomato (34,727) [2].…”

Gall-forming root-knot nematodes hijack key plant cellular functions to induce multinucleate and hypertrophied feeding cells

“…Plant responses initially were analysed by comparing un-attacked and nematode-attacked root regions (i.e., galls), with large-scale transcriptomic data providing a comprehensive view of differences in host gene expression patterns. These studies were conducted using the model plant Arabidopsis thaliana (Hammes et al, 2005;Jammes et al, 2005;Fuller & Lilley, 2007;Barcala et al, 2010), but also Medicago truncatula (Damiani et al, 2012), Solanum lycopersicum (Bar-Orl et al, 2005;Schaff et al, 2007;Fosu-Nyarko, 2009;Portillo & Lindsey, 2009), S. torvum (Bagnaresi et al, 2013), Vigna unguigulata (Das et al, 2010), Glycine max (Ibrahim et al, 2011), Arachis hypogaea (Tirumalaraju et al, 2011), and…”

Genome-Wide Analysis and Differential Expression of Chitinases in Banana Against Root Lesion Nematode (Pratylenchus coffeae) and Eumusa Leaf Spot (Mycosphaerella eumusae) Pathogens

“…The comparison all the five CIs of class I based on the sequence similarity showed no similarity between overexpressed and underexpressed CIs of class I chitinase. Bagnaresi [19] also stated that identification of nematode-induced chitinase at the sequence level helps to narrow down the choice of chitinase isoforms for introgression into susceptible crops for developing resistance against nematodes. However, when comparison of was made between NUR and NCR for the expression of these two CIs, the CI of class I was overexpressed (2.01-fold) whereas CI of class II was underexpressed (−4.4-fold) in NCR.…”

“…However, in general, induction of specific chitinase isoform in the incompatible host mostly proved to be effective against specific pathogens in several crops [16][17][18]. Therefore, it can be inferred that native and specific chitinase isoforms are highly effective to exert resistance in susceptible cultivar through transgenic approach [19]. These findings reinforces that success of developing transgenic plants in enhancing resistance to biotic stresses lies mainly on selection of specific chitinase isoforms, as each isoform may have different roles like antifungal and antifreeze activities [16,20].…”