A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.

IF 5.5 1区 生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY
Raquel Lima-Cordón, Jason Travis Mohabir, Mohini Sooklall, Aina Martinez Zurita, Meg Shieh, Cheyenne Knox, Sabrina Gobran, Zachary Johnson, Margaret Laws, Ruchit Panchal, Reza Niles-Robin, Horace Cox, Maria Eugenia Grillet, Jorge E Moreno, Socrates Herrera, Martha Quinones, Angela M Early, Jacob A Tennessen, Daniel E Neafsey
{"title":"A Short-Read Amplicon Sequencing Protocol and Bioinformatic Pipeline for Ecological Surveillance of Dipteran Disease Vectors.","authors":"Raquel Lima-Cordón, Jason Travis Mohabir, Mohini Sooklall, Aina Martinez Zurita, Meg Shieh, Cheyenne Knox, Sabrina Gobran, Zachary Johnson, Margaret Laws, Ruchit Panchal, Reza Niles-Robin, Horace Cox, Maria Eugenia Grillet, Jorge E Moreno, Socrates Herrera, Martha Quinones, Angela M Early, Jacob A Tennessen, Daniel E Neafsey","doi":"10.1111/1755-0998.14088","DOIUrl":null,"url":null,"abstract":"<p><p>Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.</p>","PeriodicalId":211,"journal":{"name":"Molecular Ecology Resources","volume":" ","pages":"e14088"},"PeriodicalIF":5.5000,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Molecular Ecology Resources","FirstCategoryId":"99","ListUrlMain":"https://doi.org/10.1111/1755-0998.14088","RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}
引用次数: 0

Abstract

Vector control remains an important strategy worldwide to prevent human infection with pathogens transmitted by arthropods. Vector control strategies rely on accurate identification of vector taxa along with vector-specific biological indicators such as feeding ecology, infection prevalence and insecticide resistance. Multiple 'DNA barcoding' protocols have been published over the past several decades to support these applications, generally relying on informal manual approaches such as BLAST to assign taxonomic identity to the resulting sequences. We present a standardised informatic pipeline for analysis of DNA barcoding data from dipteran vectors, VecTreeID, that uses short-read amplicon sequencing (AmpSeq) coupled with sequence similarity assessment (BLAST) and an evolutionary placement algorithm (EPA-ng) to achieve vector taxonomic identification, capture bionomic features (blood and plant meal sources), determine Plasmodium infection status (for anopheline mosquitoes) and detect target-site insecticide resistance mutations. The VecTreeID pipeline provides uncertainty in assignment through identifications at varying levels of taxonomic rank, a feature missing from many approaches to DNA barcoding, but important given gaps and labelling problems in public sequence databases. We validated an Illumina-based implementation of VecTreeID on laboratory and field samples, and find that the blood meal amplicons can detect vertebrate DNA sequences up to 36 h post-feeding, and that short-read sequencing data are capable of sensitively detecting minor sequences in DNA mixtures representing multi-species blood or nectar meals. This high-throughput VecTreeID approach empowers researchers and public health professionals to survey and control arthropod disease vectors consistently and effectively.

双翅目疾病媒介生态监测的短读扩增子测序方案和生物信息学管道。
病媒控制仍然是全世界预防人类感染节肢动物传播的病原体的一项重要战略。病媒控制战略依赖于准确识别病媒分类群以及病媒特异性生物指标,如摄食生态、感染流行率和杀虫剂抗性。在过去的几十年里,已经发表了多种“DNA条形码”协议来支持这些应用,通常依赖于非正式的手动方法,如BLAST来分配结果序列的分类身份。我们提出了一个标准化的信息管道,用于分析双翅目载体的DNA条形码数据,VecTreeID,该管道使用短读扩增子测序(AmpSeq),序列相似性评估(BLAST)和进化定位算法(EPA-ng)来实现载体分类鉴定,捕获生物学特征(血液和植物膳食来源),确定疟原虫感染状态(对于按蚊)并检测目标位点的杀虫剂抗性突变。VecTreeID管道通过不同分类等级的鉴定提供了分配的不确定性,这是许多DNA条形码方法所缺少的一个特征,但对于公共序列数据库中的空白和标记问题很重要。我们在实验室和现场样本上验证了基于illumina的VecTreeID实现,发现血粉扩增子可以检测脊椎动物进食后36小时的DNA序列,并且短读测序数据能够灵敏地检测代表多物种血或蜜粉的DNA混合物中的小序列。这种高通量VecTreeID方法使研究人员和公共卫生专业人员能够一致有效地调查和控制节肢动物疾病媒介。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
Molecular Ecology Resources
Molecular Ecology Resources 生物-进化生物学
CiteScore
15.60
自引率
5.20%
发文量
170
审稿时长
3 months
期刊介绍: Molecular Ecology Resources promotes the creation of comprehensive resources for the scientific community, encompassing computer programs, statistical and molecular advancements, and a diverse array of molecular tools. Serving as a conduit for disseminating these resources, the journal targets a broad audience of researchers in the fields of evolution, ecology, and conservation. Articles in Molecular Ecology Resources are crafted to support investigations tackling significant questions within these disciplines. In addition to original resource articles, Molecular Ecology Resources features Reviews, Opinions, and Comments relevant to the field. The journal also periodically releases Special Issues focusing on resource development within specific areas.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信