Deciphering the Genome-Wide Transcriptomic Changes during Interactions of Resistant and Susceptible Genotypes of American Elm with Ophiostoma novo-ulmi.

Dutch elm disease (DED), caused by Ophiostoma novo-ulmi (Onu), is a destructive disease of American elm (Ulmus americana L.). The molecular mechanisms of resistance and susceptibility against DED in American elm are still largely uncharacterized. In the present study, we performed a de novo transcriptome (RNA-sequencing; RNA-Seq) assembly of U. americana and compared the gene expression in a resistant genotype, 'Valley Forge', and a susceptible (S) elm genotype at 0 and 96 h post-inoculation of Onu. A total of 85,863 non-redundant unigenes were identified. Compared to the previously characterized U. minor transcriptome, U. americana has 35,290 similar and 55,499 unique genes. The transcriptomic variations between 'Valley Forge' and 'S' were found primarily in the photosynthesis and primary metabolism, which were highly upregulated in the susceptible genotype irrespective of the Onu inoculation. The resistance to DED was associated with the activation of RPM1-mediated effector-triggered immunity that was demonstrated by the upregulation of genes involved in the phenylpropanoids biosynthesis and PR genes. The most significantly enriched gene ontology (GO) terms in response to Onu were response to stimulus (GO:0006950), response to stress (GO:0050896), and secondary metabolic process (GO:0008152) in both genotypes. However, only in the resistant genotype, the defense response (GO:0006952) was among the topmost significantly enriched GO terms. Our findings revealed the molecular regulations of DED resistance and susceptibility and provide a platform for marker-assisted breeding of resistant American elm genotypes.

Seasonal Variation of Allergenic Acarofauna From the Homes of Allergic Rhinitis and Asthmatic Patients.

House dust mites (HDMs) play positive role in causing various kinds of allergenic manifestations such as allergic rhinitis (AR), asthma, dermatitis, and urticaria. HDMs are prevalent in temperate regions but various studies have shown the prevalence of HDMs in tropical and subtropical countries. The present study was conducted from March 2015 to February 2016. During the study period, a total of 500 dust samples were collected from 125 homes of 125 patients suffering from AR and asthma. From these 500 dust samples, 466 samples were found to be positive for mites. The year was divided into three climatic classes, i.e., CCL I (March, April, May, June), CCL II (July, August, September, October), and CCL III (November, December, January, February) A total of 7,710 mites were collected, from which 2,902 (37.63%) mites were found in samples collected during summer season, i.e., CCL-I, 3,728 (48.35%) mites were found in samples collected during rainy season, i.e., CCL-II and only 1,080 (14.01%) mites were found in samples collected during winter season, i.e., CCL-III. Total 7,710 mite specimens were isolated with 7,404, i.e., 96.03% were only from the hypoorder Astigmata, 240, i.e., 3.11% from suborder Prostigmata, 46, i.e., 0.60% from order Mesostigmata, and 20, i.e., 0.26% from suborder Oribatida. The present study indicates that Dermatophagoides pteronyssinus (Trouessart 1897) (Astigmata) was most abundant and frequently found allergenic mite species followed by D. farinae (Hughes 1961), D. microceras (Griffiths and Cunnington 1971), Acarus siro (Linnaeus 1758), Tyrophagus putrescentiae (Schrank 1781), Lepidoglyphus destructor (Schrank 1781), Euroglyphus maynei (Cooreman 1950), Cheyletus, Mesostigmatic, and Oribatida mites.

Sequencing-based high throughput mutation detection in bread wheat.

BACKGROUND: Forward genetic approaches have limited use for agronomic traits that can't be reliably scored on a single plant basis. Thus, mutants in wheat and other crops are more useful for gene function studies by reverse genetic approach. With a long-term goal to develop a sequence-based mutation detection resource in hexaploid wheat, we conducted a feasibility study to accurately differentiate induced mutations from the homoeologs' sequence variations present among the three wheat genomes. RESULTS: A reduced representation ApeKI library consisting of 21 Ethylmethane Sulfonate (EMS) induced mutants and two wild type cv. Indian plants was developed using individual barcode adapters and sequenced. A novel bioinformatics pipeline was developed to identify sequence variants using 178,464 wheat unigenes as a reference wheat transcriptome. In total, 14,130 mutational changes [Single Nucleotide Polymorphisms (SNPs) and Insertions/Deletions (INDELs)] and 150,511 homoeologous sequence changes were detected. On an average, 662 SNPs (ranging from 46 to 1,330) and 10 small INDELs (ranging from 0 to 23) were identified for each of the mutants. A mutation frequency of one per 5 Kb was observed with 70 % being transitions and 30 % transversions. The pipeline was tested using the known sequence changes in the three wheat genes. Genes present in the distal regions of the chromosomes were found to be more prone to EMS compared to genes present in the proximal regions. Redefined parameters identified a total of 28,348 mutational changes (1,349/plant). CONCLUSIONS: We conclude that sequencing based mutation detection is a valuable method to identify induced mutations at large.