Illumina paired-end whole-genome sequencing reads from isolate CA1 were quality-controlled, adapter-trimmed, assembled de novo, evaluated for assembly quality, and annotated using two complementary bacterial genome annotation pipelines: Bakta and NCBI PGAP. The trimmed paired-end reads were assembled de novo using SPAdes in isolate mode. The raw SPAdes scaffold assembly contained 221 sequences totaling 4,351,195 bp. After filtering to retain sequences ≥500 bp, the working assembly contained 22 sequences totaling 4,302,673 bp. Assembly statistics were calculated using QUAST. QUAST reported N50 of 331,662 bp, N90 of 140,099 bp, L50 of 4, L90 of 12, and GC content of 55.03% for the filtered assembly. The contig-length distribution ranged from 881,468 bp to 2,350 bp, with 22 retained scaffolds.
The final draft genome assembly contained 22 sequences, with a total length of 4,302,673 bp, GC content of approximately 55.0%, and scaffold N50 of 331,662 bp. Read-back mapping showed excellent support, with 99.89% mapped reads and 99.71% properly paired reads, indicating that the assembly is strongly supported by the original Illumina data. Genome completeness estimates were high. BUSCO using the bacterial bacteria_odb12 dataset reported 99.1% complete BUSCOs, 0.0% duplicated BUSCOs, and 0.0% missing BUSCOs. PGAP-associated CheckM output reported 97.12% completeness, 0.52% contamination, and 0.00% strain heterogeneity, supporting the interpretation that the CA1 assembly is a high-quality draft bacterial genome.
Bakta annotation predicted 3,890 CDSs, 54 tRNAs, 3 rRNAs, 1 tmRNA, 6 ncRNAs, 13 ncRNA regions, 2 pseudogenes, 183 hypothetical proteins, 8 assembly gaps, and 1 oriC. PGAP annotation produced a broadly similar annotation, with 3,882 CDS features, 3,879 translated protein products, 52 tRNAs, 3 rRNAs, 1 tmRNA, 11 regulatory/riboswitch features, and 3 pseudogene CDSs based on direct parsing of the uploaded PGAP output files. The two annotation systems therefore agree well at the genome scale, while differing slightly in gene prediction, RNA annotation, pseudogene handling, and functional naming.