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ONT-Based Draft Genome Assembly and Annotation of Alternaria atra
Bhawna Bonthala1, Corinn S Small1, Maximilian A Lutz1
1Chair of Phytopathology, School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany.
Molecular Plant-Microbe Interactions : MPMI
|March 29, 2021
Summary
This study presents the first high-quality genome assembly for Alternaria atra, a fungus known for causing crop diseases and potential biocontrol applications. This resource aids research into Alternaria evolution and its dual role as pathogen or biocontrol agent.
Area of Science:
- Mycology
- Genomics
- Plant Pathology
Background:
- Species of Alternaria are significant plant pathogens causing crop losses.
- Alternaria atra, previously Ulocladium atrum, causes Ulocladium blight and can act as a biocontrol agent against Botrytis cinerea.
Purpose of the Study:
- To provide a high-quality, scaffold-level reference genome assembly and annotation for Alternaria atra.
- To establish a genomic resource for studying the evolution and pathogenicity mechanisms within the Alternaria genus.
Main Methods:
- Scaffold-level genome assembly.
- RNA-sequencing-guided gene prediction using BRAKER.
- Functional annotation of predicted genes.
Main Results:
- A genome assembly comprising 43 scaffolds with a total length of 39.62 Mbp and scaffold N50 of 3,893,166 bp.
- Prediction of 12,173 protein-coding genes with functional annotation.
- The longest 10 scaffolds contain 89.9% of the assembled data.
Conclusions:
- The genome assembly and annotation provide a valuable resource for Alternaria research.
- Facilitates studies on the evolution of the complex Alternaria genus.
- Aids in understanding the mechanisms behind Alternaria atra's role as a pathogen or biocontrol agent.
