Oryza australiensis collapsed assembly annotation data

Structural and functional annotation data for O. australiensis collapsed genome assembly.
Transposable element repeats were identified and masked using RepeatModeler2 v2.0.5 and RepeatMasker v4.1.5 using the soft masking option. Paired-end RNAseq files were adaptor-trimmed using TrimGalore! v0.6.10 and aligned to genomes using HISAT2. Gene prediction was performed with Braker3 v3.0.3.
Functional annotation of the O. australiensis coding sequences (CDS) was performed in OmicsBox 3.1.11. Sequences were BLAST searched against a non-redundant protein sequence database using BLASTX with viridiplantae taxonomy and an e-value threshold of 1.0E-10. Sequences were run through InterProScan and Gene Ontology (GO) terms were retrieved from BLAST hits using Gene Ontology mapping with Blast2GO annotation. Blast2GO annotations were then combined with GO terms produced from InterProScan. Sequences with no BLAST hits were run through the Coding Potential Analysis Test (CPAT) in OmicsBox to search for potential coding transcripts. CPAT was run using the prebuilt A. thaliana model and with an Oryza specific model (organism: 45270 Oryza).