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

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 R...

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Published inMolecular ecology resources Vol. 20; no. 1; pp. 268 - 282
Main Authors Ma, Weihua, Zhao, Xianxin, Yin, Chuanlin, Jiang, Fan, Du, Xiaoyong, Chen, Taiyu, Zhang, Qinghua, Qiu, Lin, Xu, Hongxing, Joe Hull, J., Li, Guoliang, Sung, Wing‐Kin, Li, Fei, Lin, Yongjun
Format Journal Article
LanguageEnglish
Published England Wiley Subscription Services, Inc 01.01.2020
Subjects
Agricultural production
Assembly
Biosynthesis
Borers
Chemical pest control
Chilo suppressalis
Chromosomes
Cold
Cold tolerance
Diapause
Ecological monitoring
Ecology
fatty acid synthesis
Fatty acids
Gene families
Gene sequencing
genetic basis
genome assembly
Genomes
Glycerol
glycerol biosynthesis
Insecticide resistance
Insects
Pest control
Pesticides
Pests
RNA-mediated interference
Scaffolding
Trehalose
trehalose transport
Triglycerides
trehalose transport
Chilo suppressalis
fatty acid synthesis
genetic basis
cold tolerance
genome assembly
glycerol biosynthesis
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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 limitation, 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 encompass 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 glycerol 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.
AbstractList 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 limitation, 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 encompass 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 glycerol 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.
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 limitation, 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 N 50 of 307 kb and a scaffold N 50 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 encompass 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 glycerol 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.
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 limitation, 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 encompass 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 glycerol 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.
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 limitation, 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 N of 307 kb and a scaffold N 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 encompass 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 glycerol 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.
Author Du, Xiaoyong
Sung, Wing‐Kin
Yin, Chuanlin
Zhang, Qinghua
Jiang, Fan
Joe Hull, J.
Zhao, Xianxin
Qiu, Lin
Ma, Weihua
Chen, Taiyu
Li, Fei
Lin, Yongjun
Li, Guoliang
Xu, Hongxing
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  surname: Lin
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  organization: Huazhong Agricultural University
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Issue 1
Keywords trehalose transport
Chilo suppressalis
fatty acid synthesis
genetic basis
cold tolerance
genome assembly
glycerol biosynthesis
Language English
License 2019 John Wiley & Sons Ltd.
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1997; 25
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2001; 36
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e_1_2_9_81_1
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Snippet 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...
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...
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...
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SubjectTerms Agricultural production
Assembly
Biosynthesis
Borers
Chemical pest control
Chilo suppressalis
Chromosomes
Cold
Cold tolerance
Diapause
Ecological monitoring
Ecology
fatty acid synthesis
Fatty acids
Gene families
Gene sequencing
genetic basis
genome assembly
Genomes
Glycerol
glycerol biosynthesis
Insecticide resistance
Insects
Pest control
Pesticides
Pests
RNA-mediated interference
Scaffolding
Trehalose
trehalose transport
Triglycerides
Title A chromosome‐level genome assembly reveals the genetic basis of cold tolerance in a notorious rice insect pest, Chilo suppressalis
URI https://onlinelibrary.wiley.com/doi/abs/10.1111%2F1755-0998.13078
https://www.ncbi.nlm.nih.gov/pubmed/31482680
https://www.proquest.com/docview/2332009020/abstract/
https://search.proquest.com/docview/2284562296
Volume 20
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