Dario Trujillo, Thiago Mastrangelo, Consuelo Estevez de Jensen, Jose Carlos Verle Rodrigues, Roger Lawrie, Steven E Massey
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Here, we present a genome admixture analysis of high quality genome sequences generated from two <i>H. armigera-H. zea</i> F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% <i>H. armigera</i> for the two F1 hybrids, confirming its accuracy. Genome sequences from five <i>H. zea</i> and one <i>H. armigera</i> that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four <i>H. zea</i> genomes generated from a previous study are predicted to possess a proportion of <i>H. armigera</i> genetic material. Using unsupervised clustering to identify non-hybridized <i>H. armigera</i> and <i>H. zea</i> genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor <i>H. armigera</i> component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of <i>H. armigera-H. zea</i> hybrids, and suggest measures that will improve such analyses.</p>","PeriodicalId":517424,"journal":{"name":"Frontiers in insect science","volume":null,"pages":null},"PeriodicalIF":2.4000,"publicationDate":"2024-02-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10926370/pdf/","citationCount":"0","resultStr":"{\"title\":\"Accurate identification of <i>Helicoverpa armigera-Helicoverpa zea</i> hybrids using genome admixture analysis: implications for genomic surveillance.\",\"authors\":\"Dario Trujillo, Thiago Mastrangelo, Consuelo Estevez de Jensen, Jose Carlos Verle Rodrigues, Roger Lawrie, Steven E Massey\",\"doi\":\"10.3389/finsc.2024.1339143\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p><i>Helicoverpa armigera</i>, the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive <i>H. armigera</i> has been reported to hybridize with local populations of <i>Helicoverpa zea</i>. The correct identification of <i>H. armigera-H. zea</i> hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate <i>H. zea</i> pesticide resistance and host plant range via introgression of <i>H. armigera</i> genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two <i>H. armigera-H. zea</i> F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% <i>H. armigera</i> for the two F1 hybrids, confirming its accuracy. Genome sequences from five <i>H. zea</i> and one <i>H. armigera</i> that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four <i>H. zea</i> genomes generated from a previous study are predicted to possess a proportion of <i>H. armigera</i> genetic material. Using unsupervised clustering to identify non-hybridized <i>H. armigera</i> and <i>H. zea</i> genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor <i>H. armigera</i> component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. 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引用次数: 0
摘要
棉铃虫(Helicoverpa armigera)是世界上最重要的农作物害虫之一,正在从旧大陆的原产地向新大陆蔓延。据报道,在巴西,入侵的 H. armigera 与当地的 Helicoverpa zea 种群杂交。鉴于杂交可能会通过 H. armigera 基因的导入促进 H. zea 的杀虫剂抗性和寄主植物范围,正确鉴定 H. armigera-H. zea 杂交种对于了解受疫情影响的新大陆地区的起源、传播和未来前景非常重要。在此,我们对两个不同实验室产生的两个 H. armigera-H. zea F1 杂交种的高质量基因组序列进行了基因组混杂分析。我们的混杂分析管道预测这两个 F1 杂交种的 H. armigera 基因含量分别为 48.8% 和 48.9%,证实了其准确性。研究中生成的 5 个 H. zea 和 1 个 H. armigera 的基因组序列没有显示杂交的证据。有趣的是,我们发现在之前的研究中生成的四个 H. zea 基因组中含有一定比例的 H. armigera 遗传物质。利用无监督聚类来识别未杂交的 H. armigera 和 H. zea 基因组,共鉴定出 8511 个祖先信息标记(AIMs)。这些标记的相对频率与四个基因组中 H. armigera 的次要成分一致,但其来源仍有待确定。我们的研究表明,基因组参考数据集的大小和质量对于准确的杂交预测至关重要。因此,我们讨论了对 H. armigera-H. zea 杂交种进行基因组混杂分析的潜在误区,并提出了改进此类分析的措施。
Accurate identification of Helicoverpa armigera-Helicoverpa zea hybrids using genome admixture analysis: implications for genomic surveillance.
Helicoverpa armigera, the cotton bollworm moth, is one of the world's most important crop pests, and is spreading throughout the New World from its original range in the Old World. In Brazil, invasive H. armigera has been reported to hybridize with local populations of Helicoverpa zea. The correct identification of H. armigera-H. zea hybrids is important in understanding the origin, spread and future outlook for New World regions that are affected by outbreaks, given that hybridization can potentially facilitate H. zea pesticide resistance and host plant range via introgression of H. armigera genes. Here, we present a genome admixture analysis of high quality genome sequences generated from two H. armigera-H. zea F1 hybrids generated in two different labs. Our admixture pipeline predicts 48.8% and 48.9% H. armigera for the two F1 hybrids, confirming its accuracy. Genome sequences from five H. zea and one H. armigera that were generated as part of the study show no evidence of hybridization. Interestingly, we show that four H. zea genomes generated from a previous study are predicted to possess a proportion of H. armigera genetic material. Using unsupervised clustering to identify non-hybridized H. armigera and H. zea genomes, 8511 ancestry informative markers (AIMs) were identified. Their relative frequencies are consistent with a minor H. armigera component in the four genomes, however its origin remains to be established. We show that the size and quality of genomic reference datasets are critical for accurate hybridization prediction. Consequently, we discuss potential pitfalls in genome admixture analysis of H. armigera-H. zea hybrids, and suggest measures that will improve such analyses.