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Solanum torvum responses to the root-knot nematode Meloidogyne incognita.

Bagnaresi P, Sala T, Irdani T, Scotto C, Lamontanara A, Beretta M, Rotino GL, Sestili S, Cattivelli L, Sabatini E - BMC Genomics (2013)

Bottom Line: 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.By combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling in a non-model species.The expression profiling of S. torvum responses to nematode infection points to sesquiterpenoids and chitinases as major effectors of nematode resistance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S Protaso 302, I-29107 Fiorenzuola d’Arda, PC, Italy.

ABSTRACT

Background: Solanum 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.

Results: As 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.

Conclusions: By 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.

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Pearson correlations among eggplant samples using total vs. validated probes. Pearson’s product moment correlation for eggplant samples were computed for the entire set of probes or the subset of eggplant validated set of probes. Correlations are shown for all pairs of sample combinations.
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Figure 4: Pearson correlations among eggplant samples using total vs. validated probes. Pearson’s product moment correlation for eggplant samples were computed for the entire set of probes or the subset of eggplant validated set of probes. Correlations are shown for all pairs of sample combinations.

Mentions: Based on the above data, in order to define an high confidence pool of probes for eggplant, we selected a reasonable tradeoff between stringency and number of preserved probes: i) ratio of alignment length to oligo length >= 0.6; ii) maximum number of mismatches <= 2; iii) start of oligo alignment within the first 20 bases from 5’ oligo end. These parameters lead to 5,770 retained oligos with a mean signal of 1,525, a value well above the mean of 727 obtained when only probes with an alignment <= 40% were considered (data not shown) and is still higher than 945, the mean of all probes in the chip (Additional file 8A). To finally verify that our probe validation procedure was beneficial, we computed the Pearson’s product moment correlation values for eggplant samples. The correlation increased in most cases (14 out of 15 pair wise comparisons) when comparing validated versus total probes (Table 2 and Figure 4) as expected by removal of probes where, due to the absence of a matching transcript target, random noise prevails leading to inconsistencies among replicates [29].


Solanum torvum responses to the root-knot nematode Meloidogyne incognita.

Bagnaresi P, Sala T, Irdani T, Scotto C, Lamontanara A, Beretta M, Rotino GL, Sestili S, Cattivelli L, Sabatini E - BMC Genomics (2013)

Pearson correlations among eggplant samples using total vs. validated probes. Pearson’s product moment correlation for eggplant samples were computed for the entire set of probes or the subset of eggplant validated set of probes. Correlations are shown for all pairs of sample combinations.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3750854&req=5

Figure 4: Pearson correlations among eggplant samples using total vs. validated probes. Pearson’s product moment correlation for eggplant samples were computed for the entire set of probes or the subset of eggplant validated set of probes. Correlations are shown for all pairs of sample combinations.
Mentions: Based on the above data, in order to define an high confidence pool of probes for eggplant, we selected a reasonable tradeoff between stringency and number of preserved probes: i) ratio of alignment length to oligo length >= 0.6; ii) maximum number of mismatches <= 2; iii) start of oligo alignment within the first 20 bases from 5’ oligo end. These parameters lead to 5,770 retained oligos with a mean signal of 1,525, a value well above the mean of 727 obtained when only probes with an alignment <= 40% were considered (data not shown) and is still higher than 945, the mean of all probes in the chip (Additional file 8A). To finally verify that our probe validation procedure was beneficial, we computed the Pearson’s product moment correlation values for eggplant samples. The correlation increased in most cases (14 out of 15 pair wise comparisons) when comparing validated versus total probes (Table 2 and Figure 4) as expected by removal of probes where, due to the absence of a matching transcript target, random noise prevails leading to inconsistencies among replicates [29].

Bottom Line: 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.By combining 454 pyrosequencing and microarray technology we were able to conduct a cost-effective global transcriptome profiling in a non-model species.The expression profiling of S. torvum responses to nematode infection points to sesquiterpenoids and chitinases as major effectors of nematode resistance.

View Article: PubMed Central - HTML - PubMed

Affiliation: Consiglio per la Ricerca e la Sperimentazione in Agricoltura, Genomics Research Centre, via S Protaso 302, I-29107 Fiorenzuola d’Arda, PC, Italy.

ABSTRACT

Background: Solanum 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.

Results: As 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.

Conclusions: By 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.

Show MeSH
Related in: MedlinePlus