The Draft Genome of Yellow Stem Borer, an Agriculturally Important Pest, Provides Molecular Insights into Its Biology, Development and Specificity Towards Rice for Infestation

Abstract

Yellow stem borer (YSB), Scirpophaga incertulas (Walker) (Lepidoptera: Crambidae), a major monophagous insect pest of rice, causes significant yield losses. The rice–YSB interaction is very dynamic, making it difficult for management. The development of resistant lines has been unsuccessful as there are no effective resistant sources in the germplasm. Genome information is necessary for a better understanding of interaction with rice in terms of its recognition, response, and infestation mechanism. The draft genome of YSB is predicted to have 46,057 genes with an estimated size of 308 Mb, being correlated with the flow cytometry analysis. The existence of complex metabolic mechanisms and genes related to specific behavior was identified, being conditioned by a higher level of regulation. We deciphered the possible visual, olfactory, and gustatory mechanisms responsible for its evolution as a monophagous pest. Comparative genomic analysis revealed that YSB is unique in the way it has evolved. The obvious presence of high-immunity-related genes, well-developed RNAi machinery, and diverse effectors provides a means for developing genomic tools for its management. The identified 21,696 SSR markers can be utilized for diversity analysis of populations across the rice-growing regions. We present the first draft genome of YSB. The information emanated paves a way for biologists to design novel pest management strategies as well as for the industry to design new classes of safer and specific insecticide molecules.

Application of Biofertilizing Agents and Entomopathogenic Fungi in Lowland Rice

“…Stem borers, which lay their eggs on the exterior of plant tissues coated in saliva [35], provide an example of this. Newly hatched larvae penetrate the stem to feed on internal tissues during the vegetative and reproductive phases of plant growth, leading to the manifestation of symptoms [36]. It is noteworthy that symptoms of this stem borer attack may arise not only from S. innotata, but also from other insects such as Gryllotalpidae sp., which infests the base of the stem and root.…”

Chromosomal-Level Reference Genome of the Moth Heortia Vitessoides (Lepidoptera: Crambidae), A Major Pest of Agarwood-Producing Trees

“…These resources can be highly beneficial for elucidating the evolutionary relationships between taxa [39], deepening the understanding of detoxification mechanisms [57], and elucidating genome biology more generally, such as revealing the burst of microRNA innovation in lepidopteran lineages [73]. For Crambidae, to date, genomic resources are available for five subfamilies including Acentropinae (Parapoynx stratiotata), Crambinae (Chilo suppressalis, Diatraea saccharalis and Chrysoteuchia culmella), Pyraustinae (Ostrinia scapulalis, Ostrinia nubilalis and Leucinodes orbonalis), Schoenobiinae (Scirpophaga incertulas), and Spilomelinae (Cnaphalocrocis medinalis and Cnaphalocrocis exigua) [17,22,36,38,43,55,95,98]. H. vitessoides belongs to the subfamily Odontiinae, and despite its ecological importance, genomic resources for this moth lineage remain lacking.…”