Genome sequence of a European D. coronariae strain

The fungal pathogen Diplocarpon coronariae, the causal agent of apple blotch, poses a significant challenge in organic apple production and meadow orchards across Europe. One potential measure to restrict the spread of the disease is cultivating resistant varieties. However, understanding the reproduction and pathogenicity of the fungus is crucial for maintaining apple resistance. The recently sequenced Chinese isolate NL1 indicates that secondary metabolites play a role in host colonization. Furthermore, the rapid adaptation of the fungus to environmental conditions, including resistance, depends on sexual reproduction. While the fungus is capable of reproducing both sexually and asexually, in Europe, only asexual reproduction has been observed. The presence of alternative forms (idiomorphs) plays a crucial role in the mating of heterothallic fungi like D. coronariae. Chinese strains have been observed to exhibit the presence of two idiomorphs (MAT1.1 and MAT1.2). At present, no sequence of a European isolate is available for analysis. This study provides the first European draft genome sequence of the D. coronariae strain (DC1_JKI) from Dresden, Germany. The final draft contained 22 scaffolds with a total length of 51.5 Mbp and an N50 of 4.0 Mbp. The BUSCO analysis of genome completeness was 98.5%. Additionally, a second isolate from Japan (NBRC 30405) was sequenced for comparison of the genome. Using long-read sequencing technologies, the DNA from DC1_JKI and NBRC 30405 was sequenced using Oxford Nanopore MinION. To polish the sequences, Illumina NovaSeq sequencing (NovaSeq 6000 S4 PE150 XP) was conducted for short reads. The draft genome sequence was assembled using Canu software, resulting in the genome sequence of DC1_JKI. The data on this platform comprise 20 files. Two genome sequences have been processed. The European assembly is available in the file "genome_DC1_JKI.fasta" and the Japanese assembly in "genome_NBRC30405.fasta". The final European genome sequence was first annotated using BRAKER 1 and BRAKER 2 and the masked genome sequence, detected repetitive elements, genome annotation features, protein sequences and coding sequences are available from this collection (genome.fa.masked.gz, genome.fa.out.gz, genome.fa.tbl.gz, Diplocarpon_coronariae-families.fa.gz, Diplocarpon_coronariae-families.stk.gz, Br2_tsebra.gtf.gz, Br2_tsebra.aa.gz, Br2_tsebra.codingseq.gz). The functional annotation of was performed with InterProScan (interproscan.tsv.gz; interproscan.gff3.gz). GeMoMa pipeline was used to predict gene models using three reference datasets from species of the genus Drepanopezizaceae and two species of the order Helotiales in combination with the incorporation of the annotation from BRAKER1 and BRAKER 2. Finally the protein sequences (Galaxy32-[GeMoMa_NBRC30405_canu].fasta, Galaxy18-[GeMoMa_DC1_JKI].fasta) and the genome annotation features (Galaxy31-[GeMoMa_NBRC30405_canu].gff, Galaxy17-[GeMoMa_DC1_JKI].gff) are available from this data collection for both genome sequences. Additionally, the genomic sequences from the mitochondria of both isolates D. coronariae from Dresden (DC1_JKI) and Japan (NBRC 30405) are provided (tig00000019_Mito_DC1_JKI.fa, GeSeqJob-20240105-133611_tig00000019_Mito_DC1_JKI.gff3, tig00000344_Mito_NBTC30405.fa, GeSeqJob-20240105-134830_tig00000344_Mito_NBRC30405.gff3).引发苹果叶斑病（apple blotch）的真菌病原菌冠毛盘孢菌（Diplocarpon coronariae），对欧洲地区的有机苹果种植与草地果园生产构成严峻挑战。限制该病害扩散的潜在手段之一为种植抗病品种，但明确该真菌的繁殖特性与致病性，是维持苹果抗病性的核心前提。近期完成测序的中国分离株NL1研究表明，次级代谢产物（secondary metabolites）在宿主定殖（host colonization）过程中发挥关键作用。此外，该真菌对包括抗药性在内的环境条件的快速适应，依赖于有性生殖（sexual reproduction）过程。尽管该真菌可进行有性与无性双重生殖，但欧洲地区仅观测到无性生殖（asexual reproduction）现象。对于异宗配合真菌（heterothallic fungi）这类冠毛盘孢菌而言，交配型异型体（idiomorphs）的存在对其交配过程至关重要。现有研究观测到中国菌株同时存在两种交配型异型体（MAT1.1和MAT1.2）。截至目前，尚无欧洲分离株的基因组序列可供分析。本研究首次公布了来自德国德累斯顿的欧洲地区苹果叶斑病病原菌分离株DC1_JKI的基因组草图序列（draft genome sequence）。最终组装得到的草图包含22个支架序列（scaffolds），总长度为51.5 Mbp，N50值为4.0 Mbp。经BUSCO基因组完整性分析，基因组完整度达98.5%。此外，为开展基因组比较分析，研究人员还对另一株日本分离株NBRC 30405完成了全基因组测序。本研究采用长读长测序技术（long-read sequencing technologies），通过Oxford Nanopore MinION平台对DC1_JKI与NBRC 30405的基因组DNA进行测序；同时利用Illumina NovaSeq测序（NovaSeq 6000 S4 PE150 XP）获取短读长数据（short reads），用于序列抛光（polish）。研究使用Canu软件完成基因组草图组装，得到DC1_JKI的基因组序列。本数据集平台共提供20个文件，涵盖两组已处理完成的基因组序列：欧洲株系的组装结果存储于文件"genome_DC1_JKI.fasta"，日本株系的组装结果存储于"genome_NBRC30405.fasta"。欧洲株系的最终基因组序列首先通过BRAKER 1与BRAKER 2进行结构注释，本数据集提供了经重复序列屏蔽的基因组序列、检测到的重复元件（repetitive elements）、基因组注释特征、蛋白质序列与编码序列，对应文件包括"genome.fa.masked.gz"、"genome.fa.out.gz"、"genome.fa.tbl.gz"、"Diplocarpon_coronariae-families.fa.gz"、"Diplocarpon_coronariae-families.stk.gz"、"Br2_tsebra.gtf.gz"、"Br2_tsebra.aa.gz"、"Br2_tsebra.codingseq.gz"。功能注释（functional annotation）通过InterProScan完成，对应输出文件为"interproscan.tsv.gz"与"interproscan.gff3.gz"。研究采用GeMoMa流程，结合来自隔孢壳科（Drepanopezizaceae）3个物种以及锤舌菌目（Helotiales）2个物种的3组参考数据集，并整合BRAKER1与BRAKER2的注释结果，预测基因模型（gene models）。针对两组基因组序列，本数据集还提供了最终得到的蛋白质序列（"Galaxy32-[GeMoMa_NBRC30405_canu].fasta"、"Galaxy18-[GeMoMa_DC1_JKI].fasta"）与基因组注释特征文件（"Galaxy31-[GeMoMa_NBRC30405_canu].gff"、"Galaxy17-[GeMoMa_DC1_JKI].gff"）。此外，本数据集还提供了两株分离株——德国德累斯顿株DC1_JKI与日本株NBRC 30405的线粒体基因组序列，对应文件包括"tig00000019_Mito_DC1_JKI.fa"、"GeSeqJob-20240105-133611_tig00000019_Mito_DC1_JKI.gff3"、"tig00000344_Mito_NBRC30405.fa"、"GeSeqJob-20240105-134830_tig00000344_Mito_NBRC30405.gff3"。