Nevertheless, many biologists, especially working with non-model organisms, still suffer from non-existing or low-coverage functional annotation, or simply struggle retrieving, summarizing and querying these data.
However, it is worth remembering that even supposedly simple model organisms are still immensely complex biological regulatory systems and often do not respond to perturbations in the way expected.
Although funduscopy as a non-invasive tool is well established in the clinics, its use to survey ocular alterations in animal model organisms is still not routine.
Conversely, in spite of recent progress, a complete functional analysis of the transcriptional responses to different oxidative stresses in model organisms is still missing.
Although much basic research now focuses on more complex model organisms, E. coli still remains important in metabolic engineering and synthetic biology.
These experiments have been performed with many model organisms but we still lack empirical estimates of the rate and effects of mutation in the protists.
Despite being one of the most intensely studied model organisms, many questions still remain about the evolutionary biology and ecology of Escherichia coli.
Application of Tiling Assembly on A. thaliana, D. melanogaster, C. elegans, and S. cerevisiae identified hundreds of high-confidence novel genes, demonstrating that even in the most well-studied model organisms there are still undiscovered genes.
However, even when one-on-one RNAi experiments are feasible in model organisms, it is still laborious and costly because more than ten thousand coding and non-coding genes are typically found in an organism (e.g., approximately 20,000-25,000 genes were identified in the human genome [ 24] and approximately 25,500 genes were predicted in the Arabidopsis genome [ 25]).
Sequencing entire genomes of non-model organisms is still out of reach for most researchers but sequencing smaller subsets of the genome, like transcriptomes, provides an attractive alternative.
