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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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Heatmap of chitinase transcript abundance. Torvum and eggplant (torvum and mel prefix, respectively) transcript abundance as affected by M. incognita infection. The IDs of modulated Torvum genes (DEG) are boxed in black, while eggplant validated genes are boxed in red over the heatmap. Colored bars on the left of the heatmap mark distinct major branches in the clustering tree grouping genes with similar expression pattern. The color scale indicates the transcript abundance value (light blue indicate higher abundance value, darker blue indicates lower abundance values).
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Figure 5: Heatmap of chitinase transcript abundance. Torvum and eggplant (torvum and mel prefix, respectively) transcript abundance as affected by M. incognita infection. The IDs of modulated Torvum genes (DEG) are boxed in black, while eggplant validated genes are boxed in red over the heatmap. Colored bars on the left of the heatmap mark distinct major branches in the clustering tree grouping genes with similar expression pattern. The color scale indicates the transcript abundance value (light blue indicate higher abundance value, darker blue indicates lower abundance values).

Mentions: As shown in the bar chart in Figure 2, chitin binding, chitin-catabolic process and chitinase activity are enriched GO terms in Torvum DEGs. Figure 5 depicts an heatmap of the 25 Torvum genes annotated with the GO term ‘chitinase activity’ (GO ID = GO:0004568). Eight of these 25 genes are modulated in Torvum (ID boxed in black). Six of these are induced by infection and cluster together (pink sidebar). Intriguingly, only one probe (namely tor5_C8583, corresponding to class II chitinase) is among eggplant validated probes. This finding, while inviting caution on eggplant expression data for this cluster, indicates that, to date, no other transcripts have been reported for eggplant in this cluster suggesting that these genes might be absent or expressed at very low levels in eggplant. Thus, those chitinases may represent a group of nematode-responsive genes whose presence and/or inducibility recruitment is an exquisite feature of nematode-challenged Torvum.


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)

Heatmap of chitinase transcript abundance. Torvum and eggplant (torvum and mel prefix, respectively) transcript abundance as affected by M. incognita infection. The IDs of modulated Torvum genes (DEG) are boxed in black, while eggplant validated genes are boxed in red over the heatmap. Colored bars on the left of the heatmap mark distinct major branches in the clustering tree grouping genes with similar expression pattern. The color scale indicates the transcript abundance value (light blue indicate higher abundance value, darker blue indicates lower abundance values).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Heatmap of chitinase transcript abundance. Torvum and eggplant (torvum and mel prefix, respectively) transcript abundance as affected by M. incognita infection. The IDs of modulated Torvum genes (DEG) are boxed in black, while eggplant validated genes are boxed in red over the heatmap. Colored bars on the left of the heatmap mark distinct major branches in the clustering tree grouping genes with similar expression pattern. The color scale indicates the transcript abundance value (light blue indicate higher abundance value, darker blue indicates lower abundance values).
Mentions: As shown in the bar chart in Figure 2, chitin binding, chitin-catabolic process and chitinase activity are enriched GO terms in Torvum DEGs. Figure 5 depicts an heatmap of the 25 Torvum genes annotated with the GO term ‘chitinase activity’ (GO ID = GO:0004568). Eight of these 25 genes are modulated in Torvum (ID boxed in black). Six of these are induced by infection and cluster together (pink sidebar). Intriguingly, only one probe (namely tor5_C8583, corresponding to class II chitinase) is among eggplant validated probes. This finding, while inviting caution on eggplant expression data for this cluster, indicates that, to date, no other transcripts have been reported for eggplant in this cluster suggesting that these genes might be absent or expressed at very low levels in eggplant. Thus, those chitinases may represent a group of nematode-responsive genes whose presence and/or inducibility recruitment is an exquisite feature of nematode-challenged Torvum.

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