Agentis Biology

Abstract

We report the high-quality genome sequence of Bacillus subtilis strain AJB-001, isolated from a laboratory culture. This announcement highlights the application of a novel AI pipeline for automated genome annotation refinement, improving the accuracy of gene prediction and functional assignment compared to standard annotation workflows.

Methods

Strain AJB-001 was grown under standard laboratory conditions. DNA was extracted using a commercial kit (ExampleKit, ExampleCorp). Sequencing was performed on an Illumina NovaSeq platform, generating 150 bp paired-end reads. Reads were quality-filtered using Trimmomatic and assembled using SPAdes v3.15. Initial annotation was performed using Prokka v1.14. The resulting annotation was then processed through BioKEA's proprietary AI refinement module (AgentAnno v1.0), which uses transformer models trained on diverse genomic data to correct gene boundaries, identify missed genes, and assign functional annotations based on context and homology.

Results

The genome of B. subtilis strain AJB-001 consists of a single circular chromosome of 4,215,606 bp with a G+C content of 43.5%. The AI-refined annotation identified 4,328 protein-coding genes, 87 tRNA genes, and 30 rRNA genes. Compared to the initial Prokka annotation, the AI refinement corrected 127 gene boundaries, identified 43 previously missed genes, and improved functional assignments for 215 hypothetical proteins.

Data Availability

The complete genome sequence has been deposited in GenBank under the accession number CP123456. Raw sequencing data are available in the NCBI Sequence Read Archive under accession number SRR9876543.

Acknowledgments

This work was supported by a grant from the Fictional Foundation for Scientific Research (Grant No. FF-2024-001). We thank the BioKEA team for providing access to the AgentAnno AI annotation refinement tool.

References

1. Smith J, et al. (2023) Advances in bacterial genome annotation using artificial intelligence. J Genomics 15:123-135.
2. Johnson A, et al. (2022) SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455-477.
3. Williams B, et al. (2021) Prokka: rapid prokaryotic genome annotation. Bioinformatics 30:2068-2069.