HGTphyloDetect：促进水平基因转移的鉴定和系统发育分析,Briefings in Bioinformatics

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HGTphyloDetect：促进水平基因转移的鉴定和系统发育分析
Briefings in Bioinformatics ( IF 6.8 ) Pub Date : 2023-02-08 , DOI: 10.1093/bib/bbad035
Le Yuan _{1,

2} , Hongzhong Lu ₃ , Feiran Li ₁ , Jens Nielsen _{1,

4} , Eduard J Kerkhoven _{1,

2}

Affiliation

背景水平基因转移 (HGT) 是基因组进化、功能获得和代谢适应环境生态位的重要驱动力。鉴于基因组数据的快速增长，假定的 HGT 事件的全基因组识别变得越来越实用。然而，现有的 HGT 分析工具箱并未得到广泛使用，受限于它们无法进行系统发育重建以探索潜在的供体，以及从进化上遥远和密切相关的物种中检测 HGT。结果在这项研究中，我们开发了 HGTphyloDetect，它是一种多功能计算工具箱，将高通量分析与系统发育推理相结合，以促进对 HGT 事件的全面调查。酿酒酵母和通用念珠菌的两个案例研究证明了 HGTphyloDetect 能够高精度地识别水平获得的基因。此外，HGTphyloDetect 使系统发育分析能够说明在进化上遥远或密切相关的物种之间可能的基因传递路径。结论 HGTphyloDetect 计算工具箱的设计易于使用，可以以高吞吐量的方式准确发现 HGT 事件，错误发现率非常低。HGTphyloDetect 工具箱及其相关用户教程可在 https://github.com/SysBioChalmers/HGTphyloDetect 免费获得。HGTphyloDetect 使系统发育分析能够说明在进化上遥远或密切相关的物种之间基因传递的可能路径。结论 HGTphyloDetect 计算工具箱的设计易于使用，可以以高吞吐量的方式准确发现 HGT 事件，错误发现率非常低。HGTphyloDetect 工具箱及其相关用户教程可在 https://github.com/SysBioChalmers/HGTphyloDetect 免费获得。HGTphyloDetect 使系统发育分析能够说明在进化上遥远或密切相关的物种之间基因传递的可能路径。结论 HGTphyloDetect 计算工具箱的设计易于使用，可以以高吞吐量的方式准确发现 HGT 事件，错误发现率非常低。HGTphyloDetect 工具箱及其相关用户教程可在 https://github.com/SysBioChalmers/HGTphyloDetect 免费获得。

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HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer

Background Horizontal gene transfer (HGT) is an important driver in genome evolution, gain-of-function, and metabolic adaptation to environmental niches. Genome-wide identification of putative HGT events has become increasingly practical, given the rapid growth of genomic data. However, existing HGT analysis toolboxes are not widely used, limited by their inability to perform phylogenetic reconstruction to explore potential donors, and the detection of HGT from both evolutionarily distant and closely related species. Results In this study, we have developed HGTphyloDetect, which is a versatile computational toolbox that combines high-throughput analysis with phylogenetic inference, to facilitate comprehensive investigation of HGT events. Two case studies with Saccharomyces cerevisiae and Candida versatilis demonstrate the ability of HGTphyloDetect to identify horizontally acquired genes with high accuracy. In addition, HGTphyloDetect enables phylogenetic analysis to illustrate a likely path of gene transmission among the evolutionarily distant or closely related species. Conclusions The HGTphyloDetect computational toolbox is designed for ease of use and can accurately find HGT events with a very low false discovery rate in a high-throughput manner. The HGTphyloDetect toolbox and its related user tutorial are freely available at https://github.com/SysBioChalmers/HGTphyloDetect.

更新日期：2023-02-08

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