首页|ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

ORPA:a fast and efficient phylogenetic analysis method for constructing genome-wide alignments of organelle genomes

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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.

Ultrafast alignmentOrganelle phylogenomicsPhylogenomic conflictEfficient pipelineMultiple sequence alignment pipeline

Guiqi Bi、Xinxin Luan、Jianbin Yan

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Shenzhen Branch,Guangdong Laboratory of Lingnan Modem Agriculture,Key Laboratory of Synthetic Biology,Ministry of Agriculture and Rural Affairs,Agricultural Genomics Institute at Shenzhen,Chinese Academy of Agricultural Sciences,Shenzhen,Guangdong 518124,China

Zhengzhou Research Base,State Key Laboratory of Cotton Biology,School of Agricultural Sciences,Zhengzhou University,Zhengzhou,Henan 450001,China

国家重点研发计划Science Technology and Innovation Commission of Shenzhen Municipality of ChinaInnovation Program of Chinese Academy of Agricultural SciencesElite Young Scientists Program of CAAS

2018YFA0903200ZDSYS 20200811142605017

2024

10.1016/j.jgg.2023.08.006

遗传学报
中国遗传学会 中国科学院遗传与发育生物学研究所

遗传学报

CSTPCD
影响因子：0.821
ISSN：1673-8527
年,卷(期)：2024.51(3)
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