{"title":"针对 Nilaparvata lugens 的 RNAi 潜在候选目标的全基因组选择。","authors":"Zhang Jinshi, Li Mei, Lian Jinjin, Zhang Weilin","doi":"10.1186/s12864-024-10940-9","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Nilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study.</p><p><strong>Results: </strong>Here, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates.</p><p><strong>Conclusion: </strong>The combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates.</p>","PeriodicalId":9030,"journal":{"name":"BMC Genomics","volume":null,"pages":null},"PeriodicalIF":3.5000,"publicationDate":"2024-11-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536790/pdf/","citationCount":"0","resultStr":"{\"title\":\"Genome-wide selection of potential target candidates for RNAi against Nilaparvata lugens.\",\"authors\":\"Zhang Jinshi, Li Mei, Lian Jinjin, Zhang Weilin\",\"doi\":\"10.1186/s12864-024-10940-9\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><strong>Background: </strong>Nilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study.</p><p><strong>Results: </strong>Here, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates.</p><p><strong>Conclusion: </strong>The combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates.</p>\",\"PeriodicalId\":9030,\"journal\":{\"name\":\"BMC Genomics\",\"volume\":null,\"pages\":null},\"PeriodicalIF\":3.5000,\"publicationDate\":\"2024-11-05\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11536790/pdf/\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"BMC Genomics\",\"FirstCategoryId\":\"99\",\"ListUrlMain\":\"https://doi.org/10.1186/s12864-024-10940-9\",\"RegionNum\":2,\"RegionCategory\":\"生物学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"\",\"PubModel\":\"\",\"JCR\":\"Q2\",\"JCRName\":\"BIOTECHNOLOGY & APPLIED MICROBIOLOGY\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"BMC Genomics","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1186/s12864-024-10940-9","RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"BIOTECHNOLOGY & APPLIED MICROBIOLOGY","Score":null,"Total":0}
引用次数: 0
摘要
背景:Nilaparvata lugens 是最具破坏性的水稻害虫之一。基于 RNAi 的 N. lugens 防治提供了一种替代传统化学杀虫剂的策略。然而,选择 RNAi 防治 N. lugens 的潜在靶标仍是一项重大挑战。目前只筛选出了两个核转基因 N. lugens 抗性植物的目标基因。重要的是,在以前的研究中,通过对模式生物重要基因的了解,每次都只能筛选出一个或几个抗 N. lugens 的潜在靶基因:结果:研究人员通过同源性比较,在全基因组范围内对潜在的抗 N. lugens 靶基因进行了硅学筛选。通过基因组同源性比较,发现黑腹果蝇基因组中约有 3.5% 与 N. lugens 基因组具有保守的基因组同源性。通过利用N. lugens蛋白来搜索定义致死或不育表型的黑腹果蝇同源物,首先筛选出358个N. lugens基因作为推定靶基因。从 358 个推测靶基因中随机选择基因(NlRan 或 NlSRP54)表达 dsRNA 的转基因水稻品系增强了对 N. lugens 的抗性。经过表达检查和安全性检查,115 个 N. lugens 基因被筛选为潜在的候选靶基因:本研究的综合努力首先提供了一种基于全基因组同源性的 RNAi 抗 N. lugens 靶基因的硅学筛选方法,这不仅为在感兴趣的害虫中批量筛选潜在靶标候选基因提供了一个新机会,而且通过提供一百多个潜在靶标候选基因,将有助于在许多害虫物种中筛选 RNAi 靶标。
Genome-wide selection of potential target candidates for RNAi against Nilaparvata lugens.
Background: Nilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study.
Results: Here, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates.
Conclusion: The combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates.
期刊介绍:
BMC Genomics is an open access, peer-reviewed journal that considers articles on all aspects of genome-scale analysis, functional genomics, and proteomics.
BMC Genomics is part of the BMC series which publishes subject-specific journals focused on the needs of individual research communities across all areas of biology and medicine. We offer an efficient, fair and friendly peer review service, and are committed to publishing all sound science, provided that there is some advance in knowledge presented by the work.