Identification and distribution of the NBS-LRR gene family in the Cassava genome

Background

Plant resistance genes (R genes) exist in large families and usually contain both a nucleotide-binding site domain and a leucine-rich repeat domain, denoted NBS-LRR. The genome sequence of cassava (Manihot esculenta) is a valuable resource for analysing the genomic organization of resistance genes in this crop.

Results

With searches for Pfam domains and manual curation of the cassava gene annotations, we identified 228 NBS-LRR type genes and 99 partial NBS genes. These represent almost 1% of the total predicted genes and show high sequence similarity to proteins from other plant species. Furthermore, 34 contained an N-terminal toll/interleukin (TIR)-like domain, and 128 contained an N-terminal coiled-coil (CC) domain. 63% of the 327 R genes occurred in 39 clusters on the chromosomes. These clusters are mostly homogeneous, containing NBS-LRRs derived from a recent common ancestor.

Conclusions

This study provides insight into the evolution of NBS-LRR genes in the cassava genome; the phylogenetic and mapping information may aid efforts to further characterize the function of these predicted R genes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1554-9) contains supplementary material, which is available to authorized users.     

A Physiological and Behavioral Mechanism for Leaf Herbivore-Induced Systemic Root Resistance

Indirect plant-mediated interactions between herbivores are important drivers of community composition in terrestrial ecosystems. Among the most striking examples are the strong indirect interactions between spatially separated leaf- and root-feeding insects sharing a host plant. Although leaf feeders generally reduce the performance of root herbivores, little is known about the underlying systemic changes in root physiology and the associated behavioral responses of the root feeders. We investigated the consequences of maize (Zea mays) leaf infestation by Spodoptera littoralis caterpillars for the root-feeding larvae of the beetle Diabrotica virgifera virgifera, a major pest of maize. D. virgifera strongly avoided leaf-infested plants by recognizing systemic changes in soluble root components. The avoidance response occurred within 12 h and was induced by real and mimicked herbivory, but not wounding alone. Roots of leaf-infested plants showed altered patterns in soluble free and soluble conjugated phenolic acids. Biochemical inhibition and genetic manipulation of phenolic acid biosynthesis led to a complete disappearance of the avoidance response of D. virgifera. Furthermore, bioactivity-guided fractionation revealed a direct link between the avoidance response of D. virgifera and changes in soluble conjugated phenolic acids in the roots of leaf-attacked plants. Our study provides a physiological mechanism for a behavioral pattern that explains the negative effect of leaf attack on a root-feeding insect. Furthermore, it opens up the possibility to control D. virgifera in the field by genetically mimicking leaf herbivore-induced changes in root phenylpropanoid patterns.Insect herbivores constantly compete for plants as a primary terrestrial source of organic carbon and nitrogen (Denno et al., 1995). Consequently, resource competition is thought to be a major determinant of the distribution and abundance of insects in natural and agricultural systems (Begon et al., 2006). Recent evidence suggests, however, that in many cases, insect herbivore competition may not follow the traditional theoretical assumptions of direct interference and/or resource exploitation, but may be determined by indirect plant-mediated effects (Kaplan and Denno, 2007; Poelman et al., 2008). Among the most striking examples of indirect plant-mediated interactions is the interplay between root- and leaf-feeding insects (Blossey and Hunt-Joshi, 2003). Despite their nonoverlapping feeding niches, leaf and root herbivores determine each other’s performance through shared host plants (Bezemer and van Dam, 2005). Although root feeders can have positive or negative effects on leaf feeders (van Dam and Heil, 2011), the effect of leaf herbivores on root consumers is predominantly negative (Johnson et al., 2012; Huang et al., 2014).Despite the increasing number of examples demonstrating negative effects of leaf attack on root herbivores (Tindall and Stout, 2001; Blossey and Hunt-Joshi, 2003; Soler et al., 2007; Gill et al., 2011), the mechanisms underlying this form of systemic induced resistance remain poorly understood (Erb et al., 2008; Rasmann and Agrawal, 2008). Pieris brassicae, for instance, was found to increase glucosinolate levels in the roots, which correlated with a reduced survival of the root feeder Delia radicum (Soler et al., 2007). Understanding why root feeders perform worse on leaf-infested plants would allow for more detailed investigations regarding the adaptive and evolutionary context of the phenomenon, and may allow for its exploitation in agriculture (for instance, by triggering root resistance through targeted leaf treatments).A promising system to study the mechanisms and agroecological consequences of plant-mediated interactions between herbivores is maize (Zea mays) and its associated pests. In the field, maize is attacked by a suite of herbivores, including leaf feeders, stem borers, and root feeders. The highly specialized root-feeding larvae of the western corn rootworm Diabrotica virgifera virgifera cause significant plant damage and yield loss in the United States and Eastern Europe. Earlier studies demonstrated that D. virgifera attack increases leaf resistance against Spodoptera spp. by triggering drought stress responses (Erb et al., 2009, 2011b). In the opposite direction, leaf feeding by Spodoptera spp. caterpillars reduces D. virgifera growth and development in a sequence-specific manner in the laboratory and the field (Erb et al., 2011c; Gill et al., 2011). D. virgifera was subsequently demonstrated to avoid leaf-infested plants by detecting and responding to a reduction in root ethylene emissions (Robert et al., 2012). However, it remains unclear whether nonvolatile chemical changes in the roots of leaf-infested maize plants affect D. virgifera foraging and performance. In this study, we explored the hypothesis that leaf infestation by Spodoptera spp. caterpillars triggers a short-range avoidance response in D. virgifera. Through a combination of bioactivity-guided fractionation of root extracts and biochemical and molecular manipulation, we show that systemic changes in soluble phenylpropanoid derivatives trigger a strong avoidance response in D. virgifera. We furthermore demonstrate that this avoidance response is mediated by systemic internal signals and is triggered specifically by herbivory, suggesting that D. virgifera actively and specifically recognizes and avoids leaf-infested plants.     

Submicroscopic Deletions at 13q32.1 Cause Congenital Microcoria

Congenital microcoria (MCOR) is a rare autosomal-dominant disorder characterized by inability of the iris to dilate owing to absence of dilator pupillae muscle. So far, a dozen MCOR-affected families have been reported worldwide. By using whole-genome oligonucleotide array CGH, we have identified deletions at 13q32.1 segregating with MCOR in six families originating from France, Japan, and Mexico. Breakpoint sequence analyses showed nonrecurrent deletions in 5/6 families. The deletions varied from 35 kbp to 80 kbp in size, but invariably encompassed or interrupted only two genes: TGDS encoding the TDP-glucose 4,6-dehydratase and GPR180 encoding the G protein-coupled receptor 180, also known as intimal thickness-related receptor (ITR). Unlike TGDS which has no known function in muscle cells, GPR180 is involved in the regulation of smooth muscle cell growth. The identification of a null GPR180 mutation segregating over two generations with iridocorneal angle dysgenesis, which can be regarded as a MCOR endophenotype, is consistent with the view that deletions of this gene, with or without the loss of elements regulating the expression of neighboring genes, are the cause of MCOR.     

"6 markers/5 colors" extended white blood cell differential by flow cytometry.

Electronic white blood cell (WBC) differential by standard cytology (hematology analyzer and visual inspection of blood smears) is limited to five types and identification of abnormal cells is only qualitative, often problematic, poorly reproducible, and labour costing. We present our results on WBC differential by flow cytometry (FCM) with a 6 markers, 5 colors CD36-FITC/CD2-PE+CRTH2-PE/CD19-ECD/CD16-Cy5/CD45-Cy7 combination, on 379 subjects, with detection of 12 different circulating cell types, among them 11 were quantified. Detection of quantitative abnormalities of whole leucocytes, neutrophils, eosinophils, basophils, monocytes, or lymphocytes was comparable by FCM and by standard cytology in terms of sensitivity and specificity. FCM was better than standard cytology in detection and quantification of circulating blast cells or immature granulocytes, with a first lineage orientation in the former case. All cases of lymphocytosis, with lineage assignment, were detected by FCM. FCM identified a group of patients with excess of CD16pos monocytes as those having an inflammatory syndrome. WBC differential by FCM is at least as reliable as by standard cytology. FCM superiority consists in identification and systematic quantification of parameters that cannot be assessed by standard cytology such as lineage orientation of blast cells or lymphocytes, and expression of markers of interest such as CD16 on inflammatory monocytes.     

The stolbur phytoplasma antigenic membrane protein gene stamp is submitted to diversifying positive selection

Surface proteins play an important role in phytoplasma life cycle. The antigenic membrane protein (AMP) of 'Candidatus Phytoplasma asteris' has been shown to interact with the insect microfilaments. Due to the synteny of the groL-amp-nadE genetic locus between phytoplasma genomes, the gene stamp that encodes the antigenic membrane protein of stolbur phytoplasma has been cloned and characterized. It encodes a 157 amino acid-long protein with a predicted signal peptide and a C-terminal hydrophobic alpha-helix. STAMP was 26-40% identical to AMP of 'Candidatus Phytoplasma asteris' strains and 40% identical to AMP of 'Ca. P. japonicum'. The expression of STAMP in Escherichia. coli produced a 16 kDa peptide recognized by an anti-stolbur monoclonal antibody. Stamp was more variable than the house-keeping gene secY and the ratio between non-synonymous over synonymous mutations (dN/dS ) was 2.78 for stamp as compared to 0.64 for secY. This indicates that stamp is submitted to a positive diversifying selection pressure.     

Caldicoprobacter algeriensis sp. nov. a New Thermophilic Anaerobic, Xylanolytic Bacterium Isolated from an Algerian Hot Spring

A thermophilic anaerobic bacterium (strain TH7C1(T)) was isolated from the hydrothermal hot spring of Guelma in the northeast of Algeria. Strain TH7C1(T) stained Gram-positive, was a non-motile rod appearing singly, in pairs, or as long chains (0.7-1 × 2-6 μm(2)). Spores were never observed. It grew at temperatures between 55 and 75°C (optimum 65°C) and at pH between 6.2 and 8.3 (optimum 6.9). It did not require NaCl for growth, but tolerated it up to 5 g l(-1). Strain TH7C1(T) is an obligatory heterotroph fermenting sugars including glucose, galactose, lactose, raffinose, fructose, ribose, xylose, arabinose, maltose, mannitol, cellobiose, mannose, melibiose, saccharose, but also xylan, and pyruvate. Fermentation of sugars only occurred in the presence of yeast extract (0.1%). The end-products from glucose fermentation were acetate, lactate, ethanol, CO(2), and H(2). Nitrate, nitrite, thiosulfate, elemental sulfur, sulfate, and sulfite were not used as electron acceptors. The G+C content of the genomic DNA was 44.7 mol% (HPLC techniques). Phylogenetic analysis of the small-subunit ribosomal RNA (rRNA) gene sequence indicated that strain TH7C1(T) was affiliated to Firmicutes, order Clostridiales, family Caldicoprobacteraceae, with Caldicoprobacter oshimai (98.5%) being its closest relative. Based on phenotypic, phylogenetic, and genetic characteristics, strain TH7C1(T) is proposed as a novel species of genus Caldicoprobacter, Caldicoprobacter algeriensis, sp. nov. (strain TH7C1(T) = DSM 22661(T) = JCM 16184(T)).