Draft genome sequence of Xylaria bambusicola isolate GMP-LS, the root and basal stem rot pathogen of sugarcane in Indonesia

TL;DR

This paper presents the first draft genome of Xylaria bambusicola, a sugarcane disease-causing fungus in Indonesia.

Contribution

The study provides the first draft genome sequence of X. bambusicola using PacBio sequencing.

Findings

The genome size is 72.43 Mb and encodes 13,430 proteins.

This genome will help understand fungal pathogenesis in sugarcane.

Abstract

The first draft genome of X. bambusicola GMP-LS, the causal pathogen of the Root, and Basal Stem Rot disease in Sugarcane is presented based on single-molecule real-time PacBio sequencing. Xylaria genome (72.43 Mb) is predicted to encode 13,430 proteins and will contribute to molecular understanding of fungal pathogenesis.

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ANNOUNCEMENT

Xylaria (Sordariomycetes, Xylariales, Xylariaceae), the largest cosmopolitan genus of Ascomycota, is defined by teleomorph features such as stromatic perithecia. Xylaria species are mostly found as saprotrophs (plant debris, dung, or termite nests), whereas representation as phytopathogens is uncommon. X. bambusicola GMP-LS was isolated from Root and basal stem rot disease (RBSR)-infected sugarcane plantations in Indonesia. An X. bambusicola strain was originally described from bamboo in Taiwan (1, 2). We performed the complete de novo genome sequencing, assembly, and annotation of this important fungal pathogen of sugarcane.

Fungal isolate GMP-LS was collected and purified from stroma in infected sugarcane in PT Gundung Madu Plantations (Indonesia) and taxonomically identified as Xylaria bambusicola based on ITS and LSU rRNA sequence analyses (Fig. S1; DOI 10.5281/zenodo.10317624). High-molecular-weight genomic DNA was extracted from 7-day-old mycelial cultures in Potato dextrose media using MasterPure Yeast DNA extraction kit (Lucigen, Biosearch Technologies, Singapore). The whole-genome DNA library preparation, sequencing, and de novo assembly were performed at Macrogen, Singapore. DNA integrity and purity was checked using the picogreen method (Invitrogen) and sequencing quality inspected using FastQC (3). Short reads were generated on the Illumina Novaseq platform (Illumina, USA) using whole-genome shotgun libraries prepared with the Illumina Truseq DNA Nano kit, followed by single-molecule real-time (SMRT) sequencing using the PacBio RS II system.

A total of 9.7 billion bases from 970,008 reads generated from Sequel II platform were submitted for de novo assembly that used wtdbg2, v 2.3 (4) and polished using Arrow (5), resulting in 315 contigs with N50 value at 958,750 bp. In addition, a total of 3.42 billion bases from 22.68 million Illumina reads was applied for accurate genome sequence using 3 rounds of polishing in Pilon (v 1.21) (6). The final genome consists of 296 contigs with the length of the longest contig and N50 value being 4,992,453 bp and 959, 283 bp, respectively. The total size of X. bambusicola GMP-LS genome was 72,430,123 bp with a mean GC content of 34.9%. Benchmarking Universal Single-Copy Orthologs (BUSCO v 3) (7) homology search against eukaryote_odb10 lineage data set assessed the genome assembly completeness to be 94.90%. Standard default settings were used for the aforementioned software analyses.

Functional annotation using EggNOG-mapper version 2 (8) showed 73.45% hits mainly consisting of carbohydrate, amino acid, nucleotide, and lipid metabolism-related genes. A total of 13,665 genes (Table S1; DOI 10.5281/zenodo.10317624) were predicted of which 98.3% had hits in Uniprot, InterPro, PFAM, or TIGRFAMs database. Average length of proteins was 361 amino acids, with 192 tRNAs and 47 rRNAs predicted in the genome. Notably, it has 44 defense mechanisms and 229 signal transduction-related genes, such as the NLR family and Nacht signaling domain. A total of 400 genes for secondary metabolites synthesis, transport, and metabolism could be predicted such as polyketide synthases that can govern the pathogenicity (Table S2; DOI 10.5281/zenodo.10317624). The availability of this X. bambusicola genome will greatly enhance our knowledge of the RBSR disease mechanism and facilitate better understanding of other pathogens within the Xylariales.