Whole genome sequence and genome annotation of Colletotrichum acutatum, causal agent of anthracnose in pepper plants in South Korea.

Colletotrichum acutatum is a destructive fungal pathogen which causes anthracnose in a wide range of crops. Here we report the whole genome sequence and annotation of C. acutatum strain KC05, isolated from an infected pepper in Kangwon, South Korea. Genomic DNA from the KC05 strain was used for the whole genome sequencing using a PacBio sequencer and the MiSeq system. The KC05 genome was determined to be 52,190,760 bp in size with a G + C content of 51.73% in 27 scaffolds and to contain 13,559 genes with an average length of 1516 bp. Gene prediction and annotation were performed by incorporating RNA-Seq data. The genome sequence of the KC05 was deposited at DDBJ/ENA/GenBank under the accession number LUXP00000000.

Direct link to deposited data

Deposited data can be found here: http://www.ncbi.nlm.nih.gov/nuccore/LUXP00000000.1/

Experimental design, materials, and methods

Colletotrichum acutatum J.H. Simmonds is an ascomycete pathogenic fungus which causes the most destructive plant disease called anthracnose in a wide range of plants including vegetables, fruits, legumes, and perennial trees worldwide [1], [2], [3], [4]. In particular, C. acutatum causes severe economic losses in the production of peppers in tropical and subtropical countries [5], [6], [7], [8]. Missing genomic sequences of C. acutatum are a major hindrance to understand the development and pathogenicity of this fungus. Here we present the whole genome sequence of the C. acutatum strain KC05 isolated from an infected pepper fruit in South Korea; its mitogenome was announced recently [9].

The whole genome shotgun sequence of C. acutatum KC05 was generated using the PacBio RS II system with a PacBio Single Molecule Real-Time (SMRT) sequencer (Pacific Biosciences, Menlo Park, CA) and a MiSeq system (Illumina, San Diego, CA). A total of 3034 Mbp from a 20-kb whole genome shotgun library was sequenced by SMRT sequencing in 233,599 long single pass reads which were assembled using the hierarchical genome assembly process (HGAP) [10]. The sequence reads were assembled with an average consensus concordance of 99.97% and an average coverage depth of 49.7 ×. Low-quality contig sequences were corrected by mapping to the contigs with high quality (10,338,346 reads; 2 × 250 bp) generated from a 600-bp paired-end library using the Illumina MiSeq system. A total of 39 contigs produced by HGAP were assembled for scaffolding with the Illumina 5-kb mate-pair library sequence data using SSPACE V3.0 software [11]. The final assembly of the entire C. acutatum KC05 genome sequence was determined to be 52,190,760 bp with a G + C content of 51.73% in 27 scaffolds (minimum, 14,215 bp; maximum, 6,776,476 bp; average, 1,932,991; N, 4,416,304 bp) and was submitted to GenBank (LUXP00000000).

A total of 13,559 genes in the C. acutatum KC05 genome sequence were annotated by BLAST using the non-redundant (nr) protein database. The evidence gene data were obtained through de novo assembly of the transcriptome using Trinity v.2.06 software [12], and were mapped to the genome using PASA v2.0.1 software (http://pasapipeline.github.io/). GeneMark-ES v.4.21 [13] and EvidenceModeler pipeline v.1.1.1 software [14] were used for self-training and for combining gene predictions, respectively. A total of 13,559 gene sets were composited, with a shortest gene length of 281 bp, a largest gene length of 27,642 bp, and an average gene length of 1516 bp in C. acutatum KC05.

Nucleotide sequence accession number

This Whole Genome project of C. acutatum KC05 has been deposited at DDBJ/ENA/GenBank under the accession LUXP00000000. The version described in this paper is version LUXP01000000.

Conflict of interest

The authors declare that there is no conflict of interests with respect to the work published in this paper.

Specifications
Organism/cell line/tissue	Colletotrichum acutatum
Strain	KC05
Sequencer or array type	PacBio RS II and Illumina MiSeq system
Data format	Raw and processed
Experimental factors	DNA extracted from a field strain, no treatment
Experimental features	Genome sequencing
Consent	Data are publicly available
Sample source location	Pepper field in Chuncheon, Kangwon, South Korea