Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)

Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)

Toxic molds in the Aspergillus genus produce cancer-causing toxins (aflatoxins) whichcontaminate crops. Aspergillus flavus isolate AF36 (NRRL 18543) does not produce aflatoxin andis able to outcompete aflatoxin-producing fungi in crops. This widely-applied aflatoxinbiocontrol isolate was first found in cottonseed from Yuma, Arizona. AF36 became the firstaflatoxin biocontrol fungus. A high-quality AF36 genome assembly was previously reported, butgene annotations predicting the protein products of that AF36 genome have not beenpublished. To fill this gap, we generated high quality gene predictions for the AF36 genome byusing long read sequencing to analyze the messenger RNA of transcribed genes. Since genetranscription is a plastic process that can be different between chemical environments andthroughout development, we sampled AF36 tissue from high and low aflatoxin environments attwo time points, resulting in four tissue samples. Our pipeline predicted 15,382 transcripts and12,894 protein-encoding genes, suggesting ~20% alternative splicing on average. These highquality gene predictions will be useful for future work on the molecular biology of an importantaflatoxin biocontrol isolate.

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Bibliographic Details
Main Author: USDA-ARS (17854919)
Format: Dataset biblioteca
Published: 2023
Subjects:Genetics, raw sequence reads,
Online Access:https://figshare.com/articles/dataset/Nanopore_PCR-cDNA_sequencing_of_Aspergillus_flavus_AF36_NRRL_18543_/25091309
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id dat-usda-us-article25091309
record_format figshare
spelling dat-usda-us-article250913092023-06-16T00:00:00Z Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543) USDA-ARS (17854919) Genetics raw sequence reads Toxic molds in the Aspergillus genus produce cancer-causing toxins (aflatoxins) whichcontaminate crops. Aspergillus flavus isolate AF36 (NRRL 18543) does not produce aflatoxin andis able to outcompete aflatoxin-producing fungi in crops. This widely-applied aflatoxinbiocontrol isolate was first found in cottonseed from Yuma, Arizona. AF36 became the firstaflatoxin biocontrol fungus. A high-quality AF36 genome assembly was previously reported, butgene annotations predicting the protein products of that AF36 genome have not beenpublished. To fill this gap, we generated high quality gene predictions for the AF36 genome byusing long read sequencing to analyze the messenger RNA of transcribed genes. Since genetranscription is a plastic process that can be different between chemical environments andthroughout development, we sampled AF36 tissue from high and low aflatoxin environments attwo time points, resulting in four tissue samples. Our pipeline predicted 15,382 transcripts and12,894 protein-encoding genes, suggesting ~20% alternative splicing on average. These highquality gene predictions will be useful for future work on the molecular biology of an importantaflatoxin biocontrol isolate. 2023-06-16T00:00:00Z Dataset Dataset 10113/AF25091309 https://figshare.com/articles/dataset/Nanopore_PCR-cDNA_sequencing_of_Aspergillus_flavus_AF36_NRRL_18543_/25091309 Copyright Undetermined
institution USDA US
collection Figshare
country Estados Unidos
countrycode US
component Datos de investigación
access En linea
databasecode dat-usda-us
tag biblioteca
region America del Norte
libraryname National Agricultural Library of USDA
topic Genetics
raw sequence reads
spellingShingle Genetics
raw sequence reads
USDA-ARS (17854919)
Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
description Toxic molds in the Aspergillus genus produce cancer-causing toxins (aflatoxins) whichcontaminate crops. Aspergillus flavus isolate AF36 (NRRL 18543) does not produce aflatoxin andis able to outcompete aflatoxin-producing fungi in crops. This widely-applied aflatoxinbiocontrol isolate was first found in cottonseed from Yuma, Arizona. AF36 became the firstaflatoxin biocontrol fungus. A high-quality AF36 genome assembly was previously reported, butgene annotations predicting the protein products of that AF36 genome have not beenpublished. To fill this gap, we generated high quality gene predictions for the AF36 genome byusing long read sequencing to analyze the messenger RNA of transcribed genes. Since genetranscription is a plastic process that can be different between chemical environments andthroughout development, we sampled AF36 tissue from high and low aflatoxin environments attwo time points, resulting in four tissue samples. Our pipeline predicted 15,382 transcripts and12,894 protein-encoding genes, suggesting ~20% alternative splicing on average. These highquality gene predictions will be useful for future work on the molecular biology of an importantaflatoxin biocontrol isolate.
format Dataset
author USDA-ARS (17854919)
author_facet USDA-ARS (17854919)
author_sort USDA-ARS (17854919)
title Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
title_short Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
title_full Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
title_fullStr Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
title_full_unstemmed Nanopore PCR-cDNA sequencing of Aspergillus flavus AF36 (NRRL 18543)
title_sort nanopore pcr-cdna sequencing of aspergillus flavus af36 (nrrl 18543)
publishDate 2023
url https://figshare.com/articles/dataset/Nanopore_PCR-cDNA_sequencing_of_Aspergillus_flavus_AF36_NRRL_18543_/25091309
work_keys_str_mv AT usdaars17854919 nanoporepcrcdnasequencingofaspergillusflavusaf36nrrl18543
_version_ 1802721054980833280

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