RNA-Seq of Rice Yellow Stem Borer, Scirpophaga incertulas Reveals Molecular Insights During Four Larval Developmental Stages

The yellow stem borer (YSB), Scirpophaga incertulas is a prominent pest in the rice cultivation causing serious yield losses. The larval stage is an important stage in YSB, responsible for maximum infestation. However, limited knowledge exists on biology and mechanisms underlying 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 at 1^st, 3^rd, 5^th and 7^th larval developmental stages employing Illumina Hi-seq. High quality reads of ~229 Mb were assembled into 24,775 transcripts with an average size of 1485bp. Genes associated with various metabolic processes i.e. detoxification mechanism (CYP450, GSTs and CarEs), 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 (TFs and hormones) were differentially regulated during the developmental stages. Identification of stage specific transcripts made possible to determine the essential processes of larval development. Comparative transcriptome analysis revealed that YSB has not much evolved in detoxification mechanism but showed presence of distinct RNAi machinery. Presence of strong specific visual recognition coupled with chemosensory mechanisms supports the monophagous nature of YSB. Designed EST-SSRs will facilitate accurate estimation of genetic diversity of YSB. This is the first report on characterization of YSB transcriptome and identification of genes involved in key processes which will help researchers and industry to devise novel pest control strategies. This study opens a new avenue to develop next generation resistant rice using RNAi or genome editing approaches.

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