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Chromosome-level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)

文献类型： 外文期刊

作者： Xu, Hongxing 1 ; Zhao, Xianxin 2 ; Yang, Yajun 1 ; Chen, Xi 2 ; Mei, Yang 2 ; He, Kang 2 ; Xu, Le 2 ; Ye, Xinhai 2 ; Liu, Yi 1 ;

作者机构： 1.Zhejiang Acad Agr Sci, Inst Plant Protect & Microbiol, State Key Lab Managing Biot & Chem Treats Qual &, Hangzhou, Peoples R China

2.Zhejiang Univ, Inst Insect Sci, State Key Lab Rice Biol, Hangzhou, Peoples R China

3.Zhejiang Univ, Inst Insect Sci, Key Lab Mol Biol Crop Pathogens & Insect Pests, Minist Agr & Rural Affairs, Hangzhou, Peoples R China

4.Yunnan Acad Agr Sci, Agr Environm & Resources Inst, Kunming, Yunnan, Peoples R China

关键词： agriculture; chromosome-level assembly; comparative genomics; insects; rice leaffolder

期刊名称：MOLECULAR ECOLOGY RESOURCES （ 影响因子：7.09； 五年影响因子：8.745 ）

ISSN： 1755-098X

年卷期：

页码：

收录情况： SCI

摘要： The rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera) is an important agricultural pest that damages rice crops and other members of related grass families. C. exigua exhibits a very similar morphological phenotype and feeding behaviour to C. medinalis, another species of rice leaffolder whose genome was recently reported. However, genomic information for C. exigua remains extremely limited. Here, we used a hybrid strategy combining different sequencing technologies, including Illumina, PacBio, 10x Genomics, and Hi-C scaffolding, to generate a high-quality chromosome-level genome assembly of C. exigua. We initially obtained a 798.8 Mb assembly with a contig N50 size of 2.9 Mb, and the N50 size was subsequently increased to 25.7 Mb using Hi-C technology to anchor 1413 scaffolds to 32 chromosomes. We detected a total of 97.7% Benchmarking Universal Single-Copy Orthologues (BUSCO) in the genome assembly, which was comprised of similar to 52% repetitive sequence and annotated 14,922 protein-coding genes. Of note, the Z and W sex chromosomes were assembled and identified. A comparative genomic analysis demonstrated that despite the high synteny observed between the two rice leaffolders, the species have distinct genomic features associated with expansion and contraction of gene families and selection pressure. In summary, our chromosome-level genome assembly and comparative genomic analysis of C. exigua provide novel insights into the evolution and ecology of this rice insect pests and offer useful information for pest control.

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