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Updated: Jun 14, 2025

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Optimization and Comparative Analysis of Plant Organellar DNA Enrichment Methods Suitable for Next-generation Sequencing

Published on: July 28, 2017

Structural variation discovery in wheat using PacBio high-fidelity sequencing.

Zhiliang Zhang^1,2, Jijin Zhang^1,2, Lipeng Kang^1,2

¹State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China.

The Plant Journal : for Cell and Molecular Biology

|September 6, 2024

Summary

This summary is machine-generated.

This study optimized structural variation (SV) detection in wheat genomes using PacBio HiFi sequencing. Combining specific aligners and callers with low-coverage sequencing provides robust and accurate SV discovery.

Keywords:

PacBio SV detection high‐fidelity (HiFi) reads structural variation (SV)

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Area of Science:

Genomics
Plant Biology
Bioinformatics

Background:

Structural variations (SVs) are crucial for plant phenotypic diversity but challenging to detect.
Previous genomic technologies had limitations in comprehensively assaying complex SVs.

Purpose of the Study:

To comprehensively evaluate long-read aligners and SV callers for structural variation detection in wheat genomes.
To establish optimal workflows for SV discovery using PacBio HiFi sequencing.

Main Methods:

Applied PacBio high-fidelity (HiFi) sequencing to wheat genomes.
Evaluated mainstream long-read aligners (e.g., Winnowmap2, NGMLR) and SV callers (e.g., SVIM).
Assessed the impact of sequencing depth on SV detection accuracy.

Main Results:

Callers significantly influenced deletion discovery accuracy (87.73% variance).
Aligners (38.25%) and callers (49.32%) substantially impacted insertion accuracy variance.
Winnowmap2 and NGMLR excelled in deletion and insertion detection, respectively; SVIM showed the best overall caller performance.
Optimal SV detection was achieved by combining specific aligners and callers.
Low-coverage HiFi sequencing proved robust for high-quality SV discovery.

Conclusions:

Established optimal workflows for SV detection in wheat using low-coverage HiFi sequencing.
The findings will advance SV discovery and understanding of their biological functions in plants.
Optimized methods enhance the study of structural variations in plant genomes.