Indica rice genome assembly, annotation and mining of blast disease resistance genes

Sequence data size for rice cultivars. (XLSX 15 kb

Transcriptome profiling reveals genetic basis of disease resistance against Corynespora cassiicola in rubber tree (Hevea brasiliensis)

Corynespora leaf disease caused by Corynespora cassiicola (Berk. & Curt.) is one of the major diseases responsible for significant yield loss in rubber trees (Hevea brasiliensis). Next-generation sequencing based transcriptomic study of two rubber clones: RRII 105 (susceptible) and GT 1 (moderately resistant) were performed to understand the molecular basis of host tolerance to fungal diseases. Genes encoding disease resistance proteins, leucine-rich repeat proteins and genes involved in carbohydrate metabolic processes were significantly up-regulated in GT 1 upon infection, but were either completely suppressed or down-regulated in RRII 105. Transcription factor activity was a major molecular function triggered in both inoculated clones. Gene Ontology analysis revealed that majority of the transcripts was enriched for defense response, response to stimulus and stress. Higher expression of 118 transcripts with complete ORFs was identified in inoculated GT 1, indicating their possible role in disease resistance. In addition, both unique and common simple sequence repeats (SSRs) were identified. In silico analysis revealed 191 informative SSRs differentiating the two clones. Variant calling in control and disease GT 1 transcriptomes with reference to RRII 105 revealed over one lakh putative base substitutions. Microarray was used to validate the results obtained on transcriptional responses. Biotic stress overview from MapMan analysis revealed stronger activation of defense-related genes, receptor-like kinases and transcription factors. This study presents the first comprehensive transcriptome of resistant and susceptible rubber clones in response to C. cassiicola. The newly identified differentially regulated genes and sequence variation provide critical knowledge for understanding the genetic basis of disease resistance and marker development. Keywords: Corynespora leaf disease, Rubber tree, RNA-Seq analysis, Digital gene expression, Disease resistance protein

Genome analysis of rice-blast fungus Magnaporthe oryzae field isolates from southern India

The Indian subcontinent is the center of origin and diversity for rice (Oryza sativa L.). The O. sativa ssp. indica is a major food crop grown in India, which occupies the first and second position in area and production, respectively. Blast disease caused by Magnaporthe oryzae is a major constraint to rice production. Here, we report the analysis of genome architecture and sequence variation of two field isolates, B157 and MG01, of the blast fungus from southern India. The 40 Mb genome of B157 and 43 Mb genome of MG01 contained 11,344 and 11,733 predicted genes, respectively. Genomic comparisons unveiled a large set of SNPs and several isolate specific genes in the Indian blast isolates. Avr genes were analyzed in several sequenced Magnaporthe strains; this analysis revealed the presence of Avr-Pizt and Avr-Ace1 genes in all the sequenced isolates. Availability of whole genomes of field isolates from India will contribute to global efforts to understand genetic diversity of M. oryzae population and to track the emergence of virulent pathotypes

Additional file 7: of Indica rice genome assembly, annotation and mining of blast disease resistance genes

Frequency histograms of numbers of nuclei per channel as a function of relative fluorescence in Pisum (internal standard), Co-39, HR-12, Tetep and Tadukan. The ‘x’ and ‘y’ axes represents number of nuclei and linear fluorescence, respectively. (PPTX 298 kb

Additional file 6: of Indica rice genome assembly, annotation and mining of blast disease resistance genes

Genome sizes of indica cultivars. (XLSX 16 kb

Comprehensive analyses of genomes, transcriptomes and metabolites of neem tree

Neem (Azadirachta indica A. Juss) is one of the most versatile tropical evergreen tree species known in India since the Vedic period (1500 BC–600 BC). Neem tree is a rich source of limonoids, having a wide spectrum of activity against insect pests and microbial pathogens. Complex tetranortriterpenoids such as azadirachtin, salanin and nimbin are the major active principles isolated from neem seed. Absolutely nothing is known about the biochemical pathways of these metabolites in neem tree. To identify genes and pathways in neem, we sequenced neem genomes and transcriptomes using next generation sequencing technologies. Assembly of Illumina and 454 sequencing reads resulted in 267 Mb, which accounts for 70% of estimated size of neem genome. We predicted 44,495 genes in the neem genome, of which 32,278 genes were expressed in neem tissues. Neem genome consists about 32.5% (87 Mb) of repetitive DNA elements. Neem tree is phylogenetically related to citrus, Citrus sinensis. Comparative analysis anchored 62% (161 Mb) of assembled neem genomic contigs onto citrus chromomes. Ultrahigh performance liquid chromatography-mass spectrometry-selected reaction monitoring (UHPLC-MS/SRM) method was used to quantify azadirachtin, nimbin, and salanin from neem tissues. Weighted Correlation Network Analysis (WCGNA) of expressed genes and metabolites resulted in identification of possible candidate genes involved in azadirachtin biosynthesis pathway. This study provides genomic, transcriptomic and quantity of top three neem metabolites resource, which will accelerate basic research in neem to understand biochemical pathways

Patient experience and perceived acceptability of whole-body magnetic resonance imaging for staging colorectal and lung cancer compared with current staging scans: a qualitative study

OBJECTIVE: To describe the experience and acceptability of whole-body magnetic resonance imaging (WB-MRI) staging compared with standard scans among patients with highly suspected or known colorectal or lung cancer. DESIGN: Qualitative study using one-to-one interviews with thematic analysis. SETTING: Patients recruited from 10 hospitals in London, East and South East England between March 2013 and July 2014. PARTICIPANTS: 51 patients (31 male, age range 40-89 years), with varying levels of social deprivation, were recruited consecutively from two parallel clinical trials comparing the diagnostic accuracy and cost-effectiveness of WB-MRI with standard scans for staging colorectal and lung cancer ('Streamline-C' and 'Streamline-L'). WB-MRI was offered as an additional scan as part of the trials. RESULTS: In general WB-MRI presented a greater challenge than standard scans, although all but four patients completed the WB-MRI. Key challenges were enclosed space, noise and scan duration; reduced patient tolerance was associated with claustrophobia, pulmonary symptoms and existing comorbidities. Coping strategies facilitated scan tolerance and were grouped into (1) those intended to help with physical and emotional challenges, and (2) those focused on motivation to complete the scan, for example focusing on health benefit. Our study suggests that good staff communication could reduce anxiety and boost coping strategies. CONCLUSIONS: Although WB-MRI was perceived as more challenging than standard scans, it was sufficiently acceptable and tolerated by most patients to potentially replace them if appropriate. TRIAL REGISTRATION NUMBER: ISRCTN43958015 and ISRCTN50436483

Additional file 12: Table S5. of Genome sequencing of herb Tulsi (Ocimum tenuiflorum) unravels key genes behind its strong medicinal properties

Repeat elements identified in Tulsi genome assembly and classified in different groups of repeats