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The yellow stem borer (YSB), Scirpophaga incertulas, is a prominent pest in rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on the biology and mechanisms underlying the growth and differentiation of YSB. To understand and identify the genes involved in YSB development and infestation, so as to design pest control strategies, we performed de novo transcriptome analysis at the first, third, fifth, and seventh larval developmental stages employing Illumina Hi-seq. High-quality reads (HQR) of ~229 Mb were assembled into 24,775 transcripts with an average size of 1485 bp. Genes associated with various metabolic processes, i.e., detoxification mechanism [CYP450, GSTs, and carboxylesterases (CarEs)], RNA interference (RNAi) machinery (Dcr-1, Dcr-2, Ago-1, Ago-2, Sid-1, Sid-2, Sid-3, and Sid-1-related gene), chemoreception (CSPs, GRs, OBPs, and ORs), and regulators [transcription factors (TFs) and hormones] were differentially regulated during the developmental stages. Identification of stage-specific transcripts made it possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not evolved much with respect to the detoxification mechanism, but showed the presence of distinct RNAi machinery. The presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed expressed sequenced tags-simple-sequence repeats (EST-SSRs) will facilitate accurate estimation of the genetic diversity of YSB. This is the first report on characterization of the YSB transcriptome and the identification of genes involved in key processes, which will help researchers and industry to devise novel pest control strategies. This study also opens up a new avenue to develop next-generation resistant rice using RNAi or genome editing approaches. [ABSTRACT FROM AUTHOR]

Nucleotide binding site leucine rich repeat (NBS-LRR) gene encoding proteins are the major biotic stress resistance genes of rice and Arabidopsis thaliana. Upstream sequences of 206 entire NBS-LRR genes of Arabidopsis and 120 genes of rice were analyzed with three highly reliable motif prediction tools for enhanced accuracy of prediction and characterization of potential transcription factor binding motifs (TFBMs). A total of 36 and 30 novel, strong TFBMs were discovered from NBS-LRR genes of rice and A. thaliana, respectively. All the motifs identifed in these sequences were analyzed for their positional conservation and the possible motif network associations were also identifed. Further, the probability of the presence of motifs in these NBS-LRR genes were validated and statistically tested. Although Arabidopsis NBS-LRR sequences showed 76.3% similarity with rice sequences at motif level, the analysis revealed that rice sequences have many unique TFBMs and are more evolved in gene expression mechanisms. The study also provided a list of novel candidate motifs for these genes, which will be a good resource for experimental validation. A novel strategy of prediction of gene expression based on motif arrangement was also demonstrated in this study. The findings of this study, such as the motifs' positional conservation, architecture, etc. offered new biological insights into the role of TFBMs in the regulation of resistance genes. [ABSTRACT FROM AUTHOR]

Identification of full length genes along with upstream regulatory elements is important to understand its expression. Here, we report preparation of high titre genomic library and identification of a genomic clone containing Pi-k h gene with its complete upstream and downstream sequences from the rice blast resistant line Tetep. Structural analysis of protein revealed that Pi-k h has a central nucleotide binding site domain, leucine-rich repeats domain and a unique zinc-finger domain. Comparative analysis of Pi-k h protein sequence showed 64% and 45% similarity with the protein sequences of rice blast resistance genes Pi-b and Pi-ta, respectively. [ABSTRACT FROM AUTHOR]

Rice blast is a continuous threat in rice ecosystems across the globe; its dynamics is becoming complex in the changing climatic conditions. Host resistance is still a viable option; hence, the exploration of resistance genes and their novel alleles is indispensable. The majority of the blast resistance genes belong to nucleotide-binding site and leucine-rich repeat (LRR) domain. In the present study, diverse LRR alleles of five major blast resistance genes (Pi2, Pi9, Pib, Pita, and Pi37) were cloned from 13 different Oryza species to determine the nucleotide diversity as well as to identify the single nucleotide polymorphisms, InDels, conserved domains, and protein functional sites. Although Pi9 and Pi2 are homologous genes, significant nucleotide variations and variants in the motifs distribution were observed. Among the five genes, Pi37 showed the highest nucleotide diversity and Pita showed the least diversity. The phylogenetic groups of alleles were correlated with the identified haplotypes. The motif (xxLxLxx) was present among all the alleles of blast R gene sequences across various Oryza species, indicating its importance. The appearance of post-translational modification sites in the protein sequences of these alleles also indicates its nature of involvement in host-pathogen interactions. The present study offers clues in further understanding the molecular evolution of the LRR domain of resistance genes, which is a key determinant of host-pathogen interactions. [ABSTRACT FROM AUTHOR]