Here, we report the first whole-genome assembly of a Fusarium xylarioides race pathogenic to robusta coffee in Uganda. It comprises 55,122,624 bases and 14,552 genes. Gene ontology analysis assigned 5,720 genes to biological processes, 4,545 genes to cellular components, and 6,021 genes to molecular function.
ABSTRACT
Here, we report the first whole-genome assembly of a Fusarium xylarioides race pathogenic to robusta coffee in Uganda. It comprises 55,122,624 bases and 14,552 genes. Gene ontology analysis assigned 5,720 genes to biological processes, 4,545 genes to cellular components, and 6,021 genes to molecular function.
ANNOUNCEMENT
In Africa, coffee wilt disease (CWD) is endemic and remains an ongoing threat to coffee production (1). In Uganda, CWD causes an annual economic loss of $17 million (2). The disease is caused by a vascular fungal pathogen, Fusarium xylarioides. The pathogen has two races, each specific to a particular coffee species. Race 1 is pathogenic to robusta coffee (Coffea canephora), whereas race 2 is pathogenic to arabica coffee (Coffea arabica) (3). F. xylarioides causes coffee plants to wilt to mortality without recovering. We hereby announce the first whole-genome assembly of an F. xylarioides race pathogenic to robusta coffee in Uganda.
The culture used for sequencing was isolated from a CWD-affected robusta coffee plant in Uganda, previously deposited as a culture collection at CABI Bioscience in Wallingford, England (IMI number 379925). The fungus was grown on potato dextrose agar (CMO 139; Oxoid, England) for 5 days under 12-hour light and dark cycles at room temperature. DNA was extracted from mycelia using the plant/seed DNA miniprep kit (Zymo Research, USA) according to the manufacturer’s instructions. The purity and quantity of extracted DNA were prechecked using a spectrophotometer (Nanodrop 2000C; Thermo Scientific). The paired-end sequencing library was prepared using the TruSeq Nano DNA library prep kit. Quantity and quality of the library were checked on the Bioanalyzer 2100 (Agilent Technologies) using a high-sensitivity (HS) DNA chip, following the manufacturer’s instructions. The library was sequenced on the HiSeq 2500 Illumina platform (2 × 150-bp chemistry) to generate 10 Gb of data (67,472,516 reads). Adapter sequences were removed using Trimmomatic v0.32 (4) at a Phred score of ≥20. FastQC v0.11.5 (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) was used to check the quality of the reads.
De novo assembly of high-quality reads was accomplished using the SOAPdenovo v2.0 assembler (5). Gaps in assembled reads were closed using GapCloser v1.12, yielding a genome size of 55,122,624 bases without gaps and a G+C content of 34.37%. There were 1,521 contigs and 1,132 scaffolds of 55 Mb and an N50 value of 138,098 bp. The statistical elements of the assembly were calculated using sanger pathogen assemblystats v3.0 (https://github.com/sanger-pathogens/assembly-stats), an open-source program.
Genome assembly was assessed using the benchmarking universal single-copy orthologs (BUSCO) v3.0.2 software package (https://busco.ezlab.org/) from the OrthoDBv9 database (6) on genome mode, and it showed that the genome was 99.3% complete.
Data availability.
This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number RXHO00000000. The version described in this paper is the first version, RXHO01000000. The raw data have been deposited in the SRA under BioProject accession number PRJNA508603 and SRA accession number PRJNA508603.
ACKNOWLEDGMENTS
This research was supported by the National Agricultural Research Organization (NARO) under the Agricultural Training and advisory services (ATAAS) project funded by World Bank grant number 4769UG. All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of the World Bank.
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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 under the accession number RXHO00000000. The version described in this paper is the first version, RXHO01000000. The raw data have been deposited in the SRA under BioProject accession number PRJNA508603 and SRA accession number PRJNA508603.