Comparative analyses of genotype dependent expressed sequence tags and stress-responsive transcriptome of chickpea wilt illustrate predicted and unexpected genes and novel regulators of plant immunity

<p>Abstract</p> <p>Background</p> <p>The ultimate phenome of any organism is modulated by regulated transcription of many genes. Characterization of genetic makeup is thus crucial for understanding the molecular basis of phenotypic diversity, evolution and response to intra- and extra-cellular stimuli. Chickpea is the world's third most important food legume grown in over 40 countries representing all the continents. Despite its importance in plant evolution, role in human nutrition and stress adaptation, very little ESTs and differential transcriptome data is available, let alone genotype-specific gene signatures. Present study focuses on <it>Fusarium </it>wilt responsive gene expression in chickpea.</p> <p>Results</p> <p>We report 6272 gene sequences of immune-response pathway that would provide genotype-dependent spatial information on the presence and relative abundance of each gene. The sequence assembly led to the identification of a <it>Ca</it>Unigene set of 2013 transcripts comprising of 973 contigs and 1040 singletons, two-third of which represent new chickpea genes hitherto undiscovered. We identified 209 gene families and 262 genotype-specific SNPs. Further, several novel transcription regulators were identified indicating their possible role in immune response. The transcriptomic analysis revealed 649 non-cannonical genes besides many unexpected candidates with known biochemical functions, which have never been associated with pathostress-responsive transcriptome.</p> <p>Conclusion</p> <p>Our study establishes a comprehensive catalogue of the immune-responsive root transcriptome with insight into their identity and function. The development, detailed analysis of <it>Ca</it>EST datasets and global gene expression by microarray provide new insight into the commonality and diversity of organ-specific immune-responsive transcript signatures and their regulated expression shaping the species specificity at genotype level. This is the first report on differential transcriptome of an unsequenced genome during vascular wilt.</p

Social Touch Gesture Recognition using Random Forest and Boosting on Distinct Feature Sets

Touch is a primary nonverbal communication channel used to communicate emotions or other social messages. Despite its importance, this channel is still very little explored in the affective computing field, as much more focus has been placed on visual and aural channels. In this paper, we investigate the possibility to automatically discriminate between different social touch types. We propose five distinct feature sets for describing touch behaviours captured by a grid of pressure sensors. These features are then combined together by using the Random Forest and Boosting methods for categorizing the touch gesture type. The proposed methods were evaluated on both the HAART (7 gesture types over different surfaces) and the CoST (14 gesture types over the same surface) datasets made available by the Social Touch Gesture Challenge 2015. Well above chance level performances were achieved with a 67% accuracy for the HAART and 59% for the CoST testing datasets respectively

Data from: Comprehensive transcriptome analysis of Crocus sativus for discovery and expression of genes involved in apocarotenoid biosynthesis

Background: Crocus sativus stigmas form rich source of apocarotenoids like crocin, picrocrocin and saffranal which besides imparting color, flavour and aroma to saffron spice also have tremendous pharmacological properties. Inspite of their importance, the biosynthetic pathway of Crocus apocarotenoids is not fully elucidated. Moreover, the mechanism of their stigma specific accumulation remains unknown. Therefore, deep transcriptome sequencing of Crocus stigma and rest of the flower tissue was done to identify the genes and transcriptional regulators involved in the biosynthesis of these compounds. Results: Transcriptome of stigma and rest of the flower tissue was sequenced using Illumina Genome Analyzer IIx platform which generated 64,604,402 flower and 51,350,714 stigma reads. Sequences were assembled de novo using trinity resulting in 64,438 transcripts which were classified into 32,204 unigenes comprising of 9853 clusters and 22,351 singletons. A comprehensive functional annotation and gene ontology (GO) analysis was carried out. 58.5 % of the transcripts showed similarity to sequences present in public databases while rest could be specific to Crocus. 5789 transcripts showed similarity to transcription factors representing 76 families out of which Myb family was most abundant. Many genes involved in carotenoid/apocarotenoid pathway were identified for the first time in this study which includes zeta-carotene isomerase and desaturase, carotenoid isomerase and lycopene epsilon-cyclase. GO analysis showed that the predominant classes in biological process category include metabolic process followed by cellular process and primary metabolic process. KEGG mapping analysis indicated that pathways involved in ribosome, carbon and starch and sucrose metabolism were highly represented. Differential expression analysis indicated that key carotenoid/apocarotenoid pathway genes including phytoene synthase, phytoene desaturase and carotenoid cleavage dioxygenase 2 are enriched in stigma thereby providing molecular proof for stigma to be the site of apocarotenoid biosynthesis. Conclusions: This data would provide a rich source for understanding the carotenoid/apocarotenoid metabolism in Crocus. The database would also help in investigating many questions related to saffron biology including flower development

Phylogeny

the folder contains files which contains sequences of CCD genes and their accession numbers. it also contains alignment file and the resulting phylogenetic tre

Molecular Characterization of UGT94F2 and UGT86C4, Two Glycosyltransferases from <i>Picrorhiza kurrooa</i>: Comparative Structural Insight and Evaluation of Substrate Recognition

<div><p>Uridine diphosphate glycosyltransferases (UGTs) are pivotal in the process of glycosylation for decorating natural products with sugars. It is one of the versatile mechanisms in determining chemical complexity and diversity for the production of suite of pharmacologically active plant natural products. <i>Picrorhiza kurrooa</i> is a highly reputed medicinal herb known for its hepato-protective properties which are attributed to a novel group of iridoid glycosides known as picrosides. Although the plant is well studied in terms of its pharmacological properties, very little is known about the biosynthesis of these important secondary metabolites. In this study, we identified two family-1 glucosyltransferases from <i>P. kurrooa</i>. The full length cDNAs of UGT94F4 and UGT86C4 contained open reading frames of 1455 and 1422 nucleotides, encoding polypeptides of 484 and 473 amino acids respectively. UGT94F2 and UGT86C4 showed differential expression pattern in leaves, rhizomes and inflorescence. To elucidate whether the differential expression pattern of the two <i>Picrorhiza</i> UGTs correlate with transcriptional regulation <i>via</i> their promoters and to identify elements that could be recognized by known iridoid-specific transcription factors, upstream regions of each gene were isolated and scanned for putative <i>cis</i>-regulatory elements. Interestingly, the presence of <i>cis</i>-regulatory elements within the promoter regions of each gene correlated positively with their expression profiles in response to different phytohormones. HPLC analysis of picrosides extracted from different tissues and elicitor-treated samples showed a significant increase in picroside levels, corroborating well with the expression profile of UGT94F2 possibly indicating its implication in picroside biosynthesis. Using homology modeling and molecular docking studies, we provide an insight into the donor and acceptor specificities of both UGTs identified in this study. UGT94F2 was predicted to be an iridoid-specific glucosyltransferase having maximum binding affinity towards 7-deoxyloganetin while as UGT86C4 was predicted to be a kaempferol-specific glucosyltransferase. These are the first UGTs being reported from <i>P. kurrooa.</i></p></div

A schematic diagram of the proposed picroside pathway in <i>Picrorhiza kurrooa.</i>

<p>Picrosides are derived from geranyl diphosphate that can be synthesized both from cytoplasmic MVA and plastidic MEP pathways. CPR: cytochrome P450 reductase; G10H: geraniol 10-hydroxylase; 10 HGO: 10-hydroxygeraniol oxidoreductase; IRS: Iridoid synthase; PAL: phenylalanine ammonia-lyase; C4H: cinnamoyl 4-hydroxylase; Route I: The route leading to the biosynthesis of secologanin, Route II: The route leading to the biosynthesis to picrosides <i>via</i> catalpol. Adapted from <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073804#pone.0073804-Damtoft1" target="_blank">[62]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073804#pone.0073804-Mahmoud1" target="_blank">[63]</a>.</p

2-D representation of interactions of UGT86C4 and UGT94F2.

<p>2-D representation of the interaction figure (in pink) of kaempferol with UGT86C4 (A), and 2-D interaction figure of 7-deoxyloganetin with UGT94F2 (B).</p