Genome sequence of a European D. coronariae strain
Bibliographic record
Abstract
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).
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How this classification was reachedexpand
Full frame machine prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. The Gemma side is a direct model label for every work in the frame, read from the title-only record. The Codex side is a classifier learned from the 10,348 direct Codex labels and calibrated to design-weighted sample rates; fields without enough sample support carry no Codex call. Candidate is the union of the two sides; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels.
Distilled classifier scores by category (both heads)
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.001 |
| Meta-epidemiology (narrow) | 0.001 | 0.000 |
| Meta-epidemiology (broad) | 0.001 | 0.001 |
| Bibliometrics | 0.001 | 0.002 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.001 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.001 | 0.001 |
| Insufficient payload (model declined to judge) | 0.003 | 0.002 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one source (direct Gemma or distilled Codex), not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".