ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

Guiqi Bi; Xinxin Luan; Jianbin Yan

doi:10.1016/j.jgg.2023.08.006

ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

doi: 10.1016/j.jgg.2023.08.006

Guiqi Bi^a, ,,
Xinxin Luan^a,b,
Jianbin Yan^a, ,

a Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
b Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China

基金项目:

We sincerely thank the editors and reviewers for their valuable suggestions and comments on this study. This work was supported by the National Key R&D Program of China (2018YFA0903200), and Science Technology and Innovation Commission of Shenzhen Municipality of China (ZDSYS 20200811142605017). It was also supported by Innovation Program of Chinese Academy of Agricultural Sciences and the Elite Young Scientists Program of CAAS.

详细信息

通讯作者:
Guiqi Bi, Email addresses:biguiqi@caas.cn

Jianbin Yan, Email addresses:jianbinlab@caas.cn

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出版历程
- 收稿日期: 2023-05-29
- 修回日期: 2023-08-19
- 网络出版日期: 2023-08-25

ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

Guiqi Bi^{a
, ,},
Xinxin Luan^a,b,
Jianbin Yan^{a
, ,}

a Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology, Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
b Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Zhengzhou, Henan 450001, China

Funds:

摘要

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 in just one minute. 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 alignment /
- Organelle phylogenomics /
- Phylogenomic conflict /
- Efficient pipeline /
- Multiple sequence alignment pipeline
Abstract:
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 in just one minute. 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 alignment /
- Organelle phylogenomics /
- Phylogenomic conflict /
- Efficient pipeline /
- Multiple sequence alignment pipeline

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参考文献(20)

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ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

doi: 10.1016/j.jgg.2023.08.006

通讯作者:
Guiqi Bi, Email addresses:biguiqi@caas.cn

Jianbin Yan, Email addresses:jianbinlab@caas.cn

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ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

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ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

doi: 10.1016/j.jgg.2023.08.006

通讯作者: Guiqi Bi, Email addresses:biguiqi@caas.cn Jianbin Yan, Email addresses:jianbinlab@caas.cn

计量

出版历程

ORPA: a fast and efficient phylogenetic analysis method for constructing genomewide alignments of organelle genomes

计量

出版历程

目录

通讯作者:
Guiqi Bi, Email addresses:biguiqi@caas.cn

Jianbin Yan, Email addresses:jianbinlab@caas.cn