Genome assembly and analysis of Arachnopeziza aurata and Arachnopeziza aurelia

Saprohytic fungi of the family Arachnopezizaceae are the closest known extant relatives of the powdery mildew fungi and may hold great potential for studying genetic components of their obligate biotrophic lifestyle. Here, we established telomere-to-telomere genome assemblies for two representatives of this family, Arachnopeziza aurata and Arachnopeziza aurelia. Both species harbor 16 chromosomes at a genome size of 43.1 and 46.3 million base-pairs, respectively, which, in contrast to the transposon-enriched powdery mildew genomes, show a repeat content below 5% and signs of repeat-induced point mutation (RIP).

In this repository, I summarize the scripts and tools I used to perform the assembly of the genomes of Arachnopeziza aurata and Arachnopeziza aurelia and analyse genomic features in the assemblies. The publication can be found at Molecular Ecology Resources and the datasets are publicly available at

• zenodo
• ENA/EBI

Index

1. Genome assembly with Canu, Flye and NextDenovo, merging assemblies using quickmerge and telomere extension with teloclip.
2. Assembly quality assessments with BUSCO, Quast, and CRAQ.
3. Genome analysis.
4. Gene annotation ab initio via BRAKER.
5. Functional gene annotations.

References

Genome assembly

• Canu v2.2 Koren et al. 2017
• Flye v2.9.2 Kolmogorov et al. 2019
• NextDenovo v2.5.2 Hu et al. 2024
• quickmerkge v0.3 Manual
• BWA v0.7.17.r1188 Li & Durbin 2009
• pilon v1.24 Walker et al. 2014
• teloclip v0.0.4 Manual

Genome assembly quality assessment

• Quast v5.2.0 Gurevich et al. 2013
• BUSCO Simão et al. 2015
• compleasm Huang & Li 2023
• CRAQ v1.0.9 Li et al. 2023

Genome analysis

• NCBI Blast+ Website
• MUMmer v4.4.0 Kurtz et al. 2004
• RepeatMasker v4.0.9 Website
• TETrimmer Qian et al. 2024
• RIPCAL v2.0 Hane & Oliver 2008

Gene annotation

• BRAKER3 v3.0.8 Bruna et al. 2023
• HISAT2 Kim et al 2015
• Trimmomatic v0.39 (Bolger et al. 2014
• HMMer v3.4 Potter et al. 2018
• InterProScan v5.73-104.0 Jones et al. 2014
• TMHMM v2.0c Krogh et al. 2001
• SignalP5.0 Almagro Armenteros et al. 2019
• OrthoFinder v2.5.5 Emms & Kelly 2019

Other command-line tools

• Samtools Publication | Manual
• BEDtools v2.31.0 Publication | Manual
• gffread Manual

Plotting and statistical analysis

• R v4.3.1 R Core Team 2018