Gene annotation of<i> </i><i>Babesia ovis</i> (Israeli strain)

This dataset contains gene annotation information for a laboratory strain of Babesia ovis (Israeli strain).File Descriptionbovis_annotation_public.gff
This file contains the gene models predicted for Babesia ovisGene annotation methodsRepeat MaskingPrior to structural annotation we created a species-specific repeat library using the RepeatModeler2 v2.0.2a package. From this repeat library, identification and masking of repeat sequences present in the genome was performed using RepeatMasker v4.1.5 (available at https://www.repeatmasker.org/). With this approach, approximately 16% of the genome was masked, roughly matching the predicted repetitive fraction from k-mer frequency analysis (Figure 1).Structural annotationStructural annotation was performed on the repeat-masked genome with Braker v3.0.3 incorporating external evidence in the form of all alveolata proteins from OrthoDB v11 (https://bioinf.uni-greifswald.de/bioinf/partitioned_odb11). Redundant gene models from GeneMark.hmm3 were removed.Functional annotationThe predicted genes were functionally annotated using the NBIS functional_annotation nextflow pipeline v2.0.0 (https://github.com/NBISweden/pipelines-nextflow). Briefly, this pipeline performs similarity searches between the annotated proteins and the UniProtKB/Swiss-Prot database (downloaded on 2022-12; 568,363 proteins) using BLAST. Then it uses InterProScan to query the proteins against InterPro v59-91 databases, and merges results using AGAT v1.2.0.tRNAs and rRNAsTransfer RNAs (tRNAs) were annotated using tRNAscan-SE v2.0.12. This analysis identified 46 tRNA genes. Ribosomal RNAs (rRNAs) were annotated using barrnap v0.9 (available at https://github.com/tseemann/barrnap). This analysis identified 13 rRNA genes including 3 copies of 18S, 5.8S, and 28S rRNAs, and 4 copies of 5S.Annotation integrationThe functionally annotated gene models were combined with organelle gene predictions and tRNA and rRNA predictions into the "bovis_annotation_public.gff" file available here.The genome assembly for Babesia ovis is not included in this dataset, as it is publicly available in the National Center for Biotechnology Information (NCBI) under accession GCA_051529585.1.