ORPA: a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes
文献类型： 外文期刊
作者： Bi, Guiqi 1 ; Luan, Xinxin 1 ; Yan, Jianbin 1 ;
作者机构： 1.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Shenzhen Branch, Guangdong Lab Lingnan Modern Agr,Key Lab Synthet B, Shenzhen 518124, Guangdong, Peoples R China
2.Zhengzhou Univ, Sch Agr Sci, State Key Lab Cotton Biol, Zhengzhou Res Base, Zhengzhou 450001, Henan, Peoples R China
关键词： Ultrafast alignment; Organelle phylogenomics; Phylogenomic conflict; Efficient pipeline; Multiple sequence alignment pipeline
期刊名称：JOURNAL OF GENETICS AND GENOMICS （ 影响因子：5.9； 五年影响因子：5.9 ）
ISSN： 1673-8527
年卷期： 2024 年 51 卷 3 期
页码：
收录情况： SCI
摘要： Creating a multi-gene alignment matrix for phylogenetic analysis using organelle genomes involves aligning single-gene datasets manually, a process that can be time-consuming and prone to errors. The HomBlocks pipeline has been created to eliminate the inaccuracies arising from manual operations. The processing of a large number of sequences, however, remains a time-consuming task. To conquer this challenge, we develop a speedy and efficient method called Organelle Genomes for Phylogenetic Analysis (ORPA). ORPA can quickly generate multiple sequence alignments for whole-genome comparisons by parsing the result files of NCBI BLAST, completing the task just in 1 min. With increasing data volume, the efficiency of ORPA is even more pronounced, over 300 times faster than HomBlocks in aligning 60 high-plant chloroplast genomes. The phylogenetic tree outputs from ORPA are equivalent to HomBlocks, indicating its outstanding efficiency. Due to its speed and accuracy, ORPA can identify species-level evolutionary conflicts, providing valuable insights into evolutionary cognition. Copyright (c) 2023, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and Genetics Society of China. Published by Elsevier Limited and Science Press. All rights reserved.
- 相关文献
作者其他论文 更多>>
-
Glutathione triggers leaf-to-leaf, calcium-based plant defense signaling
作者：Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Du, Xiaoxi;Hu, Shuai;Shan, Xiaoyi;Xie, Daoxin;Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Du, Xiaoxi;Hu, Shuai;Wang, Guo-Liang;Shan, Xiaoyi;Xie, Daoxin;Li, Rui;Du, Ran;Chen, Haidong;Yan, Jianbin;Yang, Yongfang;Du, Xiaoxi;Hu, Shuai;Du, Xiaoxi;Hu, Shuai;Wang, Guo-Liang;Xie, Daoxin
关键词：
-
Multi-Omics Analyses Reveal the Red and Far-Red Light Combination Enhancing Heterologous Protein and Metabolite Production in Nicotiana benthamiana
作者：Zhang, Yating;Wang, Fengjiao;Du, Ran;Zhou, Shaoqun;Yan, Jianbin;Li, Wei;Wang, Fengjiao;Li, Tao
关键词：agroinfiltration; expression efficiency; light quality;
Nicotiana benthamiana ; synthetic biology -
Electrical and calcium signaling in plant systemic defense: from local wounds to global responses
作者：Li, Rui;Yan, Jianbin;Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Xie, Daoxin;Shan, Xiaoyi;Li, Rui;Yang, Yongfang;Lou, Hao;Wang, Weicheng;Xie, Daoxin;Shan, Xiaoyi;Yang, Yongfang
关键词：defense response; electrical and Ca2+ signals; insect feeding; long-distance transmission; mechanical wounding
-
Developing a multi-modular assembled prime editing (mPE) system improved precise multi-base insertion efficiency in dicots
作者：Lu, Pengjun;Zuo, Erwei;Yan, Jianbin
关键词：Prime editing; CRISPR; Genome editing; Dicot; Arabidopsis thaliana; Nicotiana benthamiana
-
Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses
作者：Ahmad, Bilal;Su, Ying;Hao, Yani;Razzaq, Tayyaba;Arshad, Rida;Zhang, Yi;Zhang, Yingchun;Wang, Xingyi;Huang, Guizhou;Su, Xiangnian;Hou, Ting;Yang, Xuanwen;Xu, Qi;Xu, Xiaodong;Peng, Yanling;Xiao, Hua;Zhou, Yongfeng;Su, Ying;Chu, Zhenzhou;Tian, Xinmin;Hao, Yani;Wang, Xingyi;Li, Chaochao;Jin, Zhongxin;Xu, Xiaodong;Bi, Guiqi;Chen, Chengjie;Huang, Jianfeng;Zhou, Yongfeng;Li, Chuanning;Chu, Zhenzhou;Wang, Qiuyan;Tian, Xinmin;Li, Chuanning;Chu, Zhenzhou;Wang, Qiuyan;Tian, Xinmin;Zhang, Yu;Chen, Yeyuan
关键词：
-
Mechanisms underlining Kelp (Saccharina japonica) adaptation to relative high seawater temperature
作者：Guo, Li;Liu, Hang;Pan, Xiaohui;Zong, Yanan;Feng, Leili;Liu, Fuli;Yang, Guanpin;Li, Xiaojie;Li, Yan;Luo, Shiju;Jiang, Liming;Chen, Shuxiu;Wang, Weiwei;Jiang, Liming;Liu, Fuli;Yang, Guanpin;Zhang, Linan;Bi, Guiqi;Yang, Guanpin;Yang, Guanpin;Yang, Guanpin
关键词：Saccharina japonica; High seawater temperature; Acclimation; Adaptation; Genome assembly; Genome wide association analysis; Transcriptomic analysis
-
Near telomere-to-telomere genome of the model plant Physcomitrium patens
作者：Bi, Guiqi;Yao, Jiawei;Wang, Huan;Yan, Jianbin;Dai, Junbiao;Zhao, Shijun;Ma, Yingxin;Dai, Junbiao;Zhao, Shijun;Ma, Yingxin;Dai, Junbiao;Zhao, Shijun;Sun, Yuanyuan;Hou, Xueren;Dai, Junbiao;Wang, Huan;Zhao, Mengkai;Sun, Yuanyuan;Hou, Xueren;Jiao, Yuling;Haas, Fabian B.;Varshney, Deepti;Rensing, Stefan A.;Prigge, Michael;Jiao, Yuling;Jiao, Yuling
关键词：
