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Chromosome-level genome assembly of an agricultural pest, the rice leaffolder Cnaphalocrocis exigua (Crambidae, Lepidoptera)
Molecular Ecology Resources ( IF 7.7 ) Pub Date : 2021-07-06 , DOI: 10.1111/1755-0998.13461
Hongxing Xu 1 , Xianxin Zhao 2 , Yajun Yang 1 , Xi Chen 2 , Yang Mei 2 , Kang He 2 , Le Xu 2 , Xinhai Ye 2 , Ying Liu 3 , Fei Li 2 , Zhongxian Lu 1
Affiliation  

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, 10× Genomics, and HiC 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 HiC 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 ~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.

中文翻译:

一种农业害虫的染色体水平基因组组装,水稻叶螟 Cnaphalocrocis exigua (Crabidae, Lepidoptera)

水稻叶螟(Cnaphalocrocis exigua)是一种重要的农业害虫,危害水稻作物和相关禾本科植物的其他成员。C. exigua表现出与C. medinalis非常相似的形态表型和摄食行为,C. medinalis是最近报道的另一种水稻叶片。然而,C 的基因组信息。exigua仍然非常有限。在这里,我们使用了一种结合不同测序技术的混合策略,包括 Illumina、PacBio、10X Genomics 和 Hi - C 支架,以生成高质量的C. exigua染色体水平基因组组装. 我们最初获得了一个 798.8 Mb 的组件,contig N50 大小为 2.9 Mb,随后使用 Hi - C 技术将 N50 大小增加到 25.7 Mb ,将 1413 个支架锚定到 32 条染色体上。我们在基因组组装中总共检测到 97.7% 的基准通用单拷贝直向同源物 (BUSCO),它由约 52% 的重复序列组成,并注释了 14,922 个蛋白质编码基因。值得注意的是,Z 和 W 性染色体被组装和鉴定。比较基因组分析表明,尽管在两个水稻叶片之间观察到高度同线性,但该物种具有与基因家族的扩张和收缩以及选择压力相关的独特基因组特征。总之,我们对C. exigua 的染色体水平基因组组装和比较基因组分析 为这种水稻害虫的进化和生态提供新的见解,并为害虫防治提供有用的信息。
更新日期:2021-07-06
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