Annotation files of Rhizopus arrhizus PR1 [* Cross-Reference *]

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Herold, Malte, 2025, "Annotation files of Rhizopus arrhizus PR1 [* Cross-Reference *]", https://lore.list.lu/citation?persistentId=perma:LIST.DYYXYP, LIST Open Repository, V1
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Description
Annotation files for genomic sequence of Rhizopus Arrhizus PR1 JBMUIF000000000 (Bioproject PRJNA1246581)

We annotated the genome assembly with funannotate v1.8.17 (https://doi.org/10.5281/zenodo.1134477). We masked repetitive regions with “funannotate mask” before running gene prediction with “funnanotate predict”  including the following layers of information: gene calls with Augustus (“--augustus_species oryzae”) (https://doi.org/10.1093/nar/gkl200); STAR v (https://doi.org/10.1093/bioinformatics/bts635) mappings of the RNAseq data (“--rna_bam”); de-novo assemblies of the RNAseq data generated with Spades v. 3.15.5 (https://doi.org/10.1093/gigascience/giz100) (“--transcript_evidence”). Coding quarry was not included as it led to an error “--weights codingquarry:0”. 

For functional annotation we ran “funannotate iprscan” implementing InterProScan v5.72 (https://doi.org/10.1093/bioinformatics/btu031), eggnog mapper v5 (https://doi.org/10.1093/nar/gky1085) with the following options (“-itype proteins -m diamond --sensmode very-sensitive --tax_scope 4751”), and antiSMASH v8.0.1 (https://doi.org/10.1093/nar/gkaf334) and merged the results with “funannotate annotate” utilizing “ACO2OL” as a locus tag prefix. 

Additionally, we determined mitochondrial contigs with GetOrganelle (https://doi.org/10.1186/s13059-020-02154-5) detecting one contig of 54 kb (contig_590) with 16S, 23S rRNA genes and 24 tRNAs.   (2025-08-29)
***This entry has been automatically imported via Datacite by LIST harvest scripts. Please refer to https://doi.org/10.5281/zenodo.16992954 for the original and latest version of the dataset and data downloads*** (2025-09-02)
Subject Chemistry; Earth and Environmental Sciences
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