2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
2b-RAD genotyping for population genomic studies of Chagas disease vectors: Rhodnius ecuadoriensis in Ecuador.
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用于恰加斯病载体群体基因组研究的 2b-RAD 基因分型：厄瓜多尔的 Rhodnius ecuadoriensis。
DOI：
10.1371/journal.pntd.0005710
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发表时间：
2017-07
影响因子：
3.8
通讯作者：
Llewellyn MS
中科院分区：
文献类型：
--
作者：
Hernandez-Castro LE;Paterno M;Villacís AG;Andersson B;Costales JA;De Noia M;Ocaña-Mayorga S;Yumiseva CA;Grijalva MJ;Llewellyn MS
厄瓜多尔红锥虫是厄瓜多尔南部和秘鲁北部恰加斯病（美洲锥虫病）的主要病媒。基因组学方法和下一代测序技术已成为研究种群多样性和结构的有力工具，这是病媒控制的关键考虑因素。在这里，我们评估了三种不同的2b限制性位点相关DNA （2b- rad）基因分型策略在厄瓜多尔红的有效性，以提供足够的基因组分辨率来梳理微进化过程并进行一些试点群体基因组分析。从2006年6月至2013年7月，在一个非专业实验室进行了2b-RAD方案，使用了从厄瓜多尔中部海岸和安第斯南部地区收集的20只厄瓜多尔红鼠成虫。2b-RAD测序数据在Illumina MiSeq仪器上进行，并使用STACKS de novo管道进行位点组装和单核苷酸多态性（SNP）发现分析。进行了初步种群基因组分析（全局AMOVA和贝叶斯聚类）。结果表明，2b-RAD基因分型方案对厄瓜多蠓有效，对其他蠓种也可能有效。然而，在我们生成的读取深度上，只有BcgI和CspCI限制酶提供了一些适合群体基因组分析的标记。我们的初步基因组分析在整个研究区域检测到遗传结构的信号。我们的研究结果表明，对于生成南美锥虫病病媒的高分辨率基因组数据来说，2b-RAD基因分型是一种成本效益高且方法简单的方法，具有在流行病学相关尺度上区分不同病媒种群的能力。因此，2b-RAD代表了医学昆虫学家手中一个强大的工具，他们无法获得专门的分子生物学设备。了解恰加斯病媒介（锥蝽）种群扩散情况是设计适合特定区域流行病学情况的控制措施的关键。在厄瓜多尔，厄瓜多尔红锥虫是引起恰加斯病传播关注的一个原因，因为它广泛分布于从厄瓜多尔中部海岸到南部的地区。本文采用全基因组测序（2b-RAD）方法对来自厄瓜多尔中部沿海Manabí省和南部Loja省4个群落的20个标本进行了分析，并对3种IIB型限制性内切酶的有效性进行了评估。本研究的结果表明，这种基因分型方法在厄瓜多尔红毛鼠和其他triatomine物种中是具有成本效益的。此外，初步的种群基因组分析结果发现了地理上不同的群落之间的种群结构和群落内部的遗传变异的信号。因此，2b-RAD作为测定媒介种群基因组学、动力学和传播的相对低技术解决方案显示出巨大的前景。
Rhodnius ecuadoriensis is the main triatomine vector of Chagas disease, American trypanosomiasis, in Southern Ecuador and Northern Peru. Genomic approaches and next generation sequencing technologies have become powerful tools for investigating population diversity and structure which is a key consideration for vector control. Here we assess the effectiveness of three different 2b restriction site-associated DNA (2b-RAD) genotyping strategies in R. ecuadoriensis to provide sufficient genomic resolution to tease apart microevolutionary processes and undertake some pilot population genomic analyses. The 2b-RAD protocol was carried out in-house at a non-specialized laboratory using 20 R. ecuadoriensis adults collected from the central coast and southern Andean region of Ecuador, from June 2006 to July 2013. 2b-RAD sequencing data was performed on an Illumina MiSeq instrument and analyzed with the STACKS de novo pipeline for loci assembly and Single Nucleotide Polymorphism (SNP) discovery. Preliminary population genomic analyses (global AMOVA and Bayesian clustering) were implemented. Our results showed that the 2b-RAD genotyping protocol is effective for R. ecuadoriensis and likely for other triatomine species. However, only BcgI and CspCI restriction enzymes provided a number of markers suitable for population genomic analysis at the read depth we generated. Our preliminary genomic analyses detected a signal of genetic structuring across the study area. Our findings suggest that 2b-RAD genotyping is both a cost effective and methodologically simple approach for generating high resolution genomic data for Chagas disease vectors with the power to distinguish between different vector populations at epidemiologically relevant scales. As such, 2b-RAD represents a powerful tool in the hands of medical entomologists with limited access to specialized molecular biological equipment. Understanding Chagas disease vector (triatomine) population dispersal is key for the design of control measures tailored for the epidemiological situation of a particular region. In Ecuador, Rhodnius ecuadoriensis is a cause of concern for Chagas disease transmission, since it is widely distributed from the central coast to southern Ecuador. Here, a genome-wide sequencing (2b-RAD) approach was performed in 20 specimens from four communities from Manabí (central coast) and Loja (southern) provinces of Ecuador, and the effectiveness of three type IIB restriction enzymes was assessed. The findings of this study show that this genotyping methodology is cost effective in R. ecuadoriensis and likely in other triatomine species. In addition, preliminary population genomic analysis results detected a signal of population structure among geographically distinct communities and genetic variability within communities. As such, 2b-RAD shows significant promise as a relatively low-tech solution for determination of vector population genomics, dynamics, and spread.
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DOI：
10.1111/evo.12281
发表时间：
2014-02
期刊：
Evolution; international journal of organic evolution
影响因子：
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影响因子：
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影响因子：
14.9
作者：
Bailey TL;Boden M;Buske FA;Frith M;Grant CE;Clementi L;Ren J;Li WW;Noble WS
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Noble WS
影响因子：
14.9
作者：
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通讯作者：
Martinez, I