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ARS Home » Pacific West Area » Maricopa, Arizona » U.S. Arid Land Agricultural Research Center » Pest Management and Biocontrol Research » Research » Publications at this Location » Publication #406053
Research Project: Improvement of the Aflatoxin Biocontrol Technology Based on Aspergillus flavus Population Biology, Genetics, and Crop Management Practices

Location: Pest Management and Biocontrol Research

Title: Nanopore PCR-cDNA sequencing of the biocontrol isolate Aspergillus flavus AF36 (NRRL 18543) informs gene annotation

Author
item LEGAN, ANDREW - Oak Ridge Institute For Science And Education (ORISE)
item Mehl, Hillary
item Varaksa Jr, Alexander
item Callicott, Kenneth

Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/29/2023
Publication Date: 9/20/2023
Citation: Legan, A.W., Mehl, H.L., Varaksa Jr., A.A., Callicott, K.A. 2023. Nanopore PCR-cDNA sequencing of the biocontrol isolate Aspergillus flavus AF36 (NRRL 18543) informs gene annotation. Microbiology Resource Announcements. 12. Article e00527-23. https://doi.org/10.1128/MRA.00527-23.
DOI: https://doi.org/10.1128/MRA.00527-23

Interpretive Summary: Toxic molds in the Aspergillus genus produce cancer-causing toxins (aflatoxins) which contaminate crops. Aspergillus flavus isolate AF36 (NRRL 18543) does not produce aflatoxin and is able to outcompete aflatoxin-producing fungi in crops. This widely-applied aflatoxin biocontrol isolate was first found in cottonseed from Yuma, Arizona. AF36 became the first aflatoxin biocontrol fungus. A high-quality AF36 genome assembly was previously reported, but gene annotations predicting the protein products of the AF36 genome have not been published. To fill this gap, we generated high quality gene predictions for the AF36 genome by using long read sequencing to analyze the messenger RNA of transcribed genes. Since gene transcription is a plastic process that can be different between chemical environments and throughout development, we sampled AF36 tissue from high and low aflatoxin environments at two time points, resulting in four tissue samples. Our pipeline predicted 15,382 transcripts and 12,894 protein-encoding genes, suggesting ~20% alternative splicing on average. These high quality gene predictions will be useful for future work on the molecular biology of an important aflatoxin biocontrol isolate.

Technical Abstract: Toxic molds in the Aspergillus genus synthesize carcinogenic aflatoxins which contaminate crops. The widely-applied biocontrol isolate A. flavus AF36 (NRRL 18543) has a high-quality public genome but lacks corresponding gene annotations. We generated high quality gene predictions for this isolate by using long read Nanopore PCR-cDNA sequencing.