Construction of a phylogenetic matrix:Scripts and guidelines for phylogenomics  

作　　者：Shiyu Du Yinhuan Ding Hu Li Aibing Zhang Arong Luo Chaodong Zhu Feng Zhang 

机构地区：[1]Department of Entomology,College of Plant Protection,Nanjing Agricultural University,Nanjing 210095,China [2]Department of Agronomy and Horticulture,Jiangsu Vocational College of Agriculture and Forestry,Nanjing 212400,China [3]Department of Entomology and MOA Key Lab of Pest Monitoring and Green Management,College of Plant Protection,China Agricultural University,Beijing 100193,China [4]College of Life Sciences,University of Chinese Academy of Sciences,Beijing 100049,China [5]Key Laboratory of the Zoological Systematics and Evolution,Institute of Zoology,Chinese Academy of Sciences,Beijing 100101,China

出　　处：《Zoological Systematics》2023年第2期107-116,共10页动物分类学报（英文版）

基　　金：This research was supported by the National Natural Science Foundation of China(31970434,32270470)to FZ;the Youth support project of Jiangsu Vocational College of Agriculture and Forestry(2022kj27)to YHD。

摘　　要：Phylogenomics is a new field that infers evolutionary relationships of taxa at the genome-scale level.The increment of molecular data may raise the potential bias as the limiting factor in phylogenomics.It is particularly important to explore these factors in phylogenomic analyses by simple,convenient,time-saving and(relatively)robust means.Here,we construct a set of custom scripts for USCO(universal single-copy orthologs)loci extraction,multiple sequence alignment,trimming poorly aligned regions,loci filtering and creating a concatenation matrix,prior to reconstructing the phylogenetic trees,to simplify analytical pipelines and improve the accuracy of tree estimation.These scripts employed a series of computationally efficient bioinformatic tools,and were used with a universal‘BASH’shell or visual interface by Windows-like‘drag and drop’operations in LINUX systems.Most steps in these scripts are parallelized to accelerate analyses.These new custom scripts provide a convenient analytical solution for phylogenomics data preparation,data quality control,and detection of potential analytical errors.Details and scripts usage are provided at https://github.com/xtmtd/Phylogenomics/tree/main/scripts.The virtual mirror file(.vmdk)integrates the operating system and required environment.All tools and scripts can be downloaded from https://dx.doi.org/10.6084/m9.figshare.21283026.Besides,the video introduction and“walk-through”for each script are provided at https://space.bilibili.com/319699648/channel/seriesdetail?sid=2682055.

关 键 词：Analytical bias sequence aligning and trimming loci filtering phylogenetic inference 

分 类 号：Q811.4[生物学—生物工程]