NoAC: an automatic builder for knowledge bases and query interfaces on genomes of non-model organisms

Area of Science:

• Bioinformatics
• Genomics
• Computational Biology

Background:

• Genome sequencing costs have decreased, leading to an increase in sequenced non-model organisms.
• Manual genome annotation for each new species is time-consuming and not scalable.
• Automated tools are needed to facilitate functional genome annotation for non-model organisms.

Purpose of the Study:

• To develop an automated web tool, NoAC (Non-model Organism Atlas Constructor), for constructing functional genome annotation knowledge bases.
• To enable researchers without programming skills to analyze non-model organism genomes.
• To facilitate comparative genomics and functional inference for understudied species.

Main Methods:

• NoAC utilizes orthology identification to transfer functional annotations from reference model organisms to target non-model organisms.
• Users upload gene/transcript data and select a reference organism.
• The tool infers Gene Ontology (GO) terms, protein domains, pathways, and interactions.

Main Results:

• NoAC successfully annotated over 50% of genes in the non-model organism *Phalaenopsis equestris*.
• Case studies on *Phalaenopsis equestris* genes (PeSEP2, PaMLS) revealed insights into flower development.
• Analysis of the *Bicyclus anynana* Wnt-1 gene demonstrated NoAC's utility in insect developmental biology.

Conclusions:

• NoAC significantly lowers the in silico barrier for studying non-model organisms.
• The tool provides a searchable knowledge base for functional genomics research.
• NoAC supports broader research across diverse taxonomic groups, accelerating biological insights.