A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis

Authors: MA, WEIHUA - Chinese Academy Of Sciences; JIANG, FAN - Huazhong Agricultural University; DU, XIAOYONG - Huazhong Agricultural University; CHEN, TAIYU - Chinese Academy Of Sciences; ZHANG, QUINGHUA - Chinese Academy Of Sciences; QIU, LIN - Hunan Agricultural University; Hull, Joe; LI, GUOLIANG - Huazhong Agricultural University; LI, FEI - Zhejiang University; LIN, YONGJUN - Chinese Academy Of Sciences; ZHAO, XIANXIN - Zhejiang University; YIN, CHUANLIN - Zhejiang University; XU, HONGXING - Zhejiang Academy Of Agricultural Sciences; SUNG, WING-KIN - Huazhong Agricultural University

Submitted to: Molecular Ecology Resources
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/19/2019
Publication Date: 9/3/2020
Citation: Ma, W., Jiang, F., Du, X., Chen, T., Zhang, Q., Qiu, L., Hull, J.J., Li, G., Li, F., Lin, Y., Zhao, X., Yin, C., Xu, H., Sung, W. 2020. A chromosome-level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis. Molecular Ecology Resources. 20(1):268-282. https://doi.org/10.1111/1755-0998.13078.
DOI: https://doi.org/10.1111/1755-0998.13078

Interpretive Summary: Although insects are unable to generate sufficient metabolic heat for maintaining thermal homeostasis, a number of species have developed various strategies to survive harsh winter conditions. Among these strategies is freeze tolerance, which utilizes diverse molecular pathways and proteins to protect cellular membranes from the effects of ice formation. The rice stem borer, a major pest of rice production that has a wide geographic range including many northern climates, is an example of one such freeze-tolerant insect. The molecular basis of freeze tolerance in this species, however, has not been fully developed as genomic resources are limited. To address this deficiency, the rice stem borer genome was sequenced and the expression of genes associated in other species with cold tolerance was evaluated under varying thermal conditions. The combined datasets will provide a valuable foundational resource for more focused, hypothesis-driven studies examining the specific molecular underpinnings of cold tolerance in the rice stem borer and related insects. Furthermore, the availability of genomic resource for this pest species is expected to facilitate the development of novel control strategies.

Technical Abstract: The rice stem borer, Chilo suppressalis, is one of the most damaging insect pests to rice production worldwide. Although C. suppressalis has been the focus of numerous studies examining cold tolerance and diapause, plant–insect interactions, pesticide targets and resistance, and the development of RNAi-mediated pest management, the absence of a high-quality genome has limited deeper insights. To address this limi- tation, we generated a draft C. suppressalis genome constructed from both Illumina and PacBio sequences. The assembled genome size was 824.35 Mb with a contig N50 of 307 kb and a scaffold N50 of 1.75 Mb. Hi-C scaffolding assigned 99.2% of the bases to one of 29 chromosomes. Based on universal single-copy orthologues (BUSCO), the draft genome assembly was estimated to be 97% complete and is predicted to en- compass 15,653 protein-coding genes. Cold tolerance is an extreme survival strategy found in animals. However, little is known regarding the genetic basis of the winter ecology of C. suppressalis. Here, we focused our orthologous analysis on those gene families associated with animal cold tolerance. Our finding provided the first genomic evidence revealing specific cold-tolerant strategies in C. suppressalis, including those involved in glucose-originated glycerol biosynthesis, triacylglycerol-originated glyc- erol biosynthesis, fatty acid synthesis and trehalose transport-intermediate cold tolerance. The high-quality C. suppressalis genome provides a valuable resource for research into a broad range of areas in molecular ecology, and subsequently benefits developing modern pest control strategies.