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

Abstract

The cost of sequencing a genome has become affordable for many research groups. However, with the growing number of sequenced genomes from non-model organisms, manually building functional genome annotation knowledge databases for each species is no longer feasible. To address this, we developed NoAC (Non-model Organism Atlas Constructor), a web tool that automatically constructs knowledge bases and query interfaces for non-model organism genomes without programming skills. In NoAC, users simply upload the gene or transcript information of a given non-model organism genome and select an appropriate reference model organism. NoAC then identifies orthologous genes, infers functional annotations, and sets up a searchable knowledge base. Functional annotations for the non-model organism such as gene ontology (GO) terms, protein domains, pathways, and physical/genetic interactors are predicted and transferred from the reference organism to the target genome. In an example non-model organism Phalaenopsis equestris, NoAC associates functional annotations for more than half of its 21,938 genes. Through case studies of the non-model organism Phalaenopsis equestris, we demonstrated that the knowledge base constructed by NoAC can reveal key functional aspects of PeSEP2 and PaMLS, supporting the study of novel genes involved in flower development. Another case study on the gene Wnt-1 in Bicyclus anynana further illustrates the applicability of NoAC in investigating insect segmentation and morphogen activity, highlighting its broader utility across diverse taxonomic genomes. In summary, NoAC allows general researchers to study non-model organisms with minimal in silico barriers. NoAC and its user tutorial are freely available at https://github.com/cosbi-nckuee/NoAC/.

Keywords: genome knowledge base; non-model organism; ortholog.