ABSTRACT
Beauveria bassiana, a well-known entomopathogenic fungus, has a worldwide distribution; however, genomes of isolates from the Neotropical region are scarce. Here, we report the draft genome sequences of eight B. bassiana isolates from Costa Rica, Puerto Rico, and Honduras.
ANNOUNCEMENT
The fungus Beauveria bassiana is a well-known biocontrol agent with a global distribution and a wide range of hosts (1). Several B. bassiana genomes have been reported, mostly from Asia (2–7). Here, we report the genome assemblies of eight isolates from Central America and the Caribbean. B. bassiana has an important role in agricultural ecosystems in the tropics (8), but more studies are needed to understand its ecological and genetic diversity (9).
We report five fungal isolates from Costa Rica, two from Puerto Rico, and one from Honduras, available at the Entomopathogenic Fungi Collection (EFC) at the National University of Costa Rica (UNA). A previous characterization suggested high diversity within the eight isolates (10).
A standard chloroform-isoamyl alcohol DNA extraction was performed using 100 mg of 10- to 15-day-old monosporic mycelia grown on potato dextrose agar (PDA) (11). Libraries were prepared using a WaferGen robotic DNA library prep. Whole-genome sequencing was performed at the Center for Genomic Research and Biocomputing at Oregon State University using a 2 × 150-bp paired-end HiSeq 3000 Illumina platform (Illumina, Inc., San Diego, CA), according to the manufacturer’s protocol at 50× coverage.
Data quality and adapter removal were done with FastQC and Trimmomatic v0.38 (12), respectively. Arguments used for Trimmomatic: TruSeq2-PE.fa as adapters file, leading and trailing were set as 3, sliding window was set at 4:15, and minlen was set at 36.
De novo assembly was performed with SPAdes v3.13.1 (13, 14), and genome assemblies were compared and evaluated using Quast v5.0.2 (15) against the Beauveria bassiana ARSEF 2860 (GenBank accession no. ADAH00000000.1). BUSCO v3.0.1 (16) was implemented to check for genome completeness against eukaryota_odb9, using Fusarium as the species argument. BUSCO results were relatively homogenous throughout the genomes.
For draft optimization of the assembled genomes, Scaffolder MeDuSa v1.6 (17) was used against B. bassiana ARSEF 8028 (GenBank assembly no. GCA_001682635.1) and Bv062 (GenBank assembly no. GCA_003337105.1). Gene calling for these improved assemblies was done using Augustus v2.6.1 against an Aspergillus oryzae training set. The genome assemblies provided in this study ranged from 32.1 to 34.8 Mb, genome completeness was estimated to be 82.23 to 86.94%, and predicted coding proteins ranged between 9,500 and 10,453 (Table 1). These assemblies and their annotations will aid insecticidal mechanism exploitations tailored toward Neotropical pest management and biotech applications.
TABLE 1.
Summary statistics for the genome assembly of eight B. bassiana isolates of Neotropical origin
| Isolate | Genome size (Mb) | Total no. of reads | No. of contigs | N50 Mb | % G +C content | % of BUSCO conserved gene set for eukaryote Fusarium graminearum | No of predicted proteins | GenBank accession no. |
|---|---|---|---|---|---|---|---|---|
| BV-ECA0 | 32.8 | 24,821,590 | 420 | 2.07 | 50.70 | 97 | 9,593 | JACVNG000000000 |
| BV-ECA1 | 33 | 31,240,515 | 877 | 2.94 | 50.71 | 97 | 9,636 | JACVNF000000000 |
| BV-ECA13 | 32.8 | 22,937,002 | 202 | 3.90 | 50.69 | 96 | 9,566 | JACVNE000000000 |
| BV-ECA26 | 32.16 | 39,078,169 | 76 | 1.10 | 50.79 | 97 | 9,465 | JACVND000000000 |
| BV-ECA27 | 32.97 | 41,021,666 | 614 | 1.49 | 50.71 | 97 | 9,648 | JACVNC000000000 |
| BV-ECA31 | 33 | 27,655,085 | 69 | 1.43 | 50.08 | 97 | 9,546 | JACVNB000000000 |
| BV-ECA43 | 34.5 | 27,606,205 | 551 | 0.89 | 50.62 | 97 | 10,210 | JACVNA000000000 |
| BV-ECA44 | 34.8 | 26,336,978 | 1,118 | 0.95 | 50.61 | 97 | 10,453 | JACVMZ000000000 |
| ARSEF 2860 | 33.6 | NAa | 1,229 | 0.73 | 51.50 | NA | 10,364 | ADAH00000000.1 |
| ARSEF 8028 | 33.6 | NA | 1,229 | 0.73 | 51.50 | NA | 10,210 | GCA_001682635.1 |
NA, not applicable.
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank (Table 1). The versions described correspond to the first version. Illumina sequence data were deposited under accession no. SRR12774113 to SRR12774120 (BioProject no. PRJNA658593).
ACKNOWLEDGMENTS
We are thankful to Allan González-Herrera from the School of Agrarian Sciences at UNA for providing the EFC-UNA isolates, to Maykol Phillips, Centro de Gestión Tecnológica (CGT) director at UNA, for setting up the computational infrastructure at LABAP and to Richard Gregory from the University of Liverpool for data storage and analysis facilities.
This research was supported by Fondos Especiales para la Educación Superior (FEES) of the Consejo Nacional de Rectores (CONARE), Costa Rica (grant agreement ACUERDO-VI-265-2016 and ACUERDO-VI-16-2018), registered at University of Costa Rica as project 801-B6-653.
This work has been submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Sciences of Ruth M. Castro-Vásquez.
Contributor Information
Stefany Solano-González, Email: stefany.solano.gonzalez@una.cr.
Antonis Rokas, Vanderbilt University.
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Associated Data
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Data Availability Statement
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank (Table 1). The versions described correspond to the first version. Illumina sequence data were deposited under accession no. SRR12774113 to SRR12774120 (BioProject no. PRJNA658593).