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WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations
Yongzhi Yang1,2, Ying Li2, Qiao Chen2
1CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, 666303, Yunnan, China.
BMC Bioinformatics
|February 15, 2019
Summary
WGDdetector is a new bioinformatic tool for identifying whole genome duplication (WGD) events using either genome or transcriptome data. This method enhances WGD detection accuracy across diverse species.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Identifying whole genome duplication (WGD) is crucial in genomics.
- Existing software is limited to high-quality genomes, ignoring transcriptomes and low-quality genomes.
- Transcriptomes offer potential for WGD detection via dS-based methods.
Purpose of the Study:
- To develop a universal tool, WGDdetector, for WGD detection.
- To enable WGD detection using both genome and transcriptome annotations.
- To utilize dS-based methods for WGD identification.
Main Methods:
- Developed the WGDdetector pipeline.
- Integrated gene family construction, dS estimation, and phasing.
- Processed paralog pairs to output dS values.
Main Results:
- Tested WGDdetector on four diverse species: Arabidopsis thaliana, Juglans regia, Populus trichocarpa, and Xenopus laevis.
- Achieved high accuracy in WGD detection using both genome and transcriptome data.
- Demonstrated practicability across herb, wood, and animal species.
Conclusions:
- WGDdetector is reliable and stable for genome data analysis.
- It provides a novel approach for WGD detection using transcriptome data.
- The tool is freely available for Windows and Linux.
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