Draft genome sequence data of Cercospora kikuchii, a causal agent of Cercospora leaf blight and purple seed stain of soybeans

Cercospora kikuchii (Tak. Matsumoto & Tomoy.) M.W. Gardner 1927 is an ascomycete fungal pathogen that causes Cercospora leaf blight and purple seed stain on soybean. Here, we report the first draft genome sequence and assembly of this pathogen. The C. kikuchii strain ARG_18_001 was isolated from soybean purple seed collected from San Pedro, Buenos Aires, Argentina, during the 2018 harvest. The genome was sequenced using a 2 × 150 bp paired-end method by Illumina NovaSeq 6000. The C. kikuchii protein-coding genes were predicted using FunGAP (Fungal Genome Annotation Pipeline). The draft genome assembly was 33.1 Mb in size with a GC-content of 53%. The gene prediction resulted in 14,856 gene models/14,721 protein coding genes. Genomic data of C. kikuchii presented here will be a useful resource for future studies of this pathosystem. The data can be accessed at GenBank under the accession number VTAY00000000 https://www.ncbi.nlm.nih.gov/nuccore/VTAY00000000.


Bioinformatics
Fungal pathogens presented here will be a useful resource for future studies of this pathosystem. The data can be accessed at GenBank under the accession number VTAY00000000 https://www.ncbi.nlm.nih.gov/ nuccore/VTAY00000000.
© 2019 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY license (http://creativecommons. org/licenses/by/4.0/).

Data
We present the draft genome assembly and gene prediction of the fungus C. kikuchii, causal agent of Cercospora leaf blight (CLB) and purple seed stain (PSS) of soybean. Recently, multi-locus phylogenetic studies confirmed that CLB and PSS is a disease complex caused by several Cercospora species. Phylogenetic analyses of cercosporoid fungi isolated from infected soybean in Argentina, Brazil and the USA determined that the species C. kikuchii, C. cf. flagellaris and C. cf. sigesbeckiae are causal agents of these diseases [1,2]. More recently, C. cf. nicotianae isolated from soybean leaves in Bolivia has been identified as a species in association with CLB [3]. A maximum-likelihood phylogenetic tree of Cercospora species was inferred in RAxML using seven nuclear loci, with data from isolate ARG_18_001 sliced from the genome assembly. The strain ARG_18_001 nested within the clade that includes other isolates of C. kikuchii, including the ex-type, with 97% bootstrap support (Fig. 1).
A total of 33,107,531 reads were assembled de novo, resulting in 136 scaffolds of at least 500 bp with the largest scaffold 3,211,885 bp and an N50 value of 898,622 bp. The mean coverage of the total assembly was 196.72-fold. The G þ C content was 53.04%. The gene prediction resulted in This Whole Genome Shotgun project has been deposited at DDBJ/ENA/GenBank under the accession VTAY00000000 https://www.ncbi.nlm.nih.gov/nuccore/VTAY00000000. The version described in this paper is version VTAY00000000.1 https://www.ncbi.nlm. nih.gov/nuccore/VTAY00000000.

Value of the Data
The first draft genome of Cercospora kikuchii ARG_18_001. C. kikuchii is an important pathogen of soybean, but the biology of this fungus is poorly understood. Genomic data presented here will be a useful resource for the study of this pathosystem. This draft genome will help in the search for genetic resistance in soybean lines 14,856 gene models with 14,721 protein coding genes and 135 non coding RNAs, including the mitochondrial genome (Table 1). The distribution of protein annotations are summarized in Table 2,  and Table 3 provides the summary statistics of the identified repetitive elements. The distribution of functional gene ontology (GO) terms from the annotated C. kikuchii ARG_18_001 genes are illustrated in Fig. 2. The distribution of species from the top BLAST hit of the predicted protein coding genes is shown in Fig. 3.

Genomic DNA extraction and sequencing
Cercospora kikuchii strain ARG_18_001 was isolated from a single conidium from soybean seeds of variety DM62R63 sampled that exhibited symptoms of purple seed stain during the 2018 harvest in San Pedro, Buenos Aires, Argentina. The isolation technique is described in [4]. This strain was deposited in the fungal culture collection of the Department of Plant Pathology, School of Agriculture, University of Buenos Aires (FAUBA, Argentina). Genomic DNA was isolated from hyphal tissue grown in potato dextrose broth for four days in darkness and constant agitation. The DNA extraction was carried out at the Institute of Microbiology and Agricultural Zoology (IMYZA -INTA) using a modified   cetyltrimethylammonium bromide (CTAB) extraction protocol developed by [5]. Total DNA was quantified by fluorometry using a Picogreen dsDNA dye kit (Quant-iT, Invitrogen, by Life Technologies, CA, USA) with a Victor 3 plate reader. Paired-end whole-genome shotgun libraries were constructed using the TruSeq Nano DNA (insert size 350 bp) library preparation kit following Illumina (San Diego, CA) protocols. Sequencing was performed using a NovaSeq 6000 sequencing system (Illumina) and yielded 65,202,278 reads.