Location: Food and Feed Safety ResearchTitle: Genome sequence of an Aspergillus flavus CA14 strain that is widely used in gene function studies
Submitted to: Microbiology Resource Announcements
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/22/2019
Publication Date: 8/15/2019
Citation: Chang, P.-K., Scharfenstein, L.L., Mack, B.M., Hua, S.T. 2019. Genome sequence of an Aspergillus flavus CA14 strain that is widely used in gene function studies. Microbiology Resource Announcements. 8(33):e00837-19. https://doi.org/10.1128/MRA.00837-19.
Interpretive Summary: Aspergillus flavus is both a plant pathogen and an opportunistic human pathogen. It can produce carcinogenic aflatoxin that adversely impacts human health and the economy. Here, we report the genome sequence of an A. flavus strain that has been widely used in gene function studies. The sequence information will benefit A. flavus functional genomics in terms of studies on fungal development, secondary metabolite production, and fungus-host plant interaction.
Technical Abstract: The CA14 strain was grown in potato dextrose broth, and genomic DNA was purified using a Quick-DNA Fungal/Bacterial Kit. DNA libraries were prepared with a NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® , and sequencing was performed on an Illumina MiSeq v2 machine with 250 bp paired-end reads. Approximate nine million paired reads were obtained. Adapters and low quality sequences were removed from the reads using BBDuk (version 3/30/17). Genome assembly of high-quality sequence reads was carried out using SPAdes (version 3.10.1) with k-mer sizes of 21, 33, 55, 77, 99, and 127. The assembled genome had a total size of 37.7 Mb with a G+C content of 47.4%. The number of predicted proteins is 12,846. The total number of contigs is 199 with an N50 of 1.3 Mb and an L50 of 8. antiSMASH fungal version 5.0 was used to identify secondary metabolite gene clusters in the CA14 genome; 28 gene clusters were found. An analysis with SMURF identified a total of 77 secondary metabolite biosynthesis backbone genes. Alignment of CA14 and NRRL3357 genome sequences with Mauve showed that a large 1.5 Mb segment of the NRRL3357 genome, corresponding to a portion on chromosome 3 of the closely related Aspergillus oryzae RIB40, was split into 277 kb, 433 kb and 716 kb, respectively, and translocated to three locations in the CA14 genome. Another 478 kb genome segment of NRRL3357 corresponding to two split segments of 290 kb and 196 kb were also translocated.