Model organism databases are in jeopardy

PomBase: a Global Core Biodata Resource-growth, collaboration, and sustainability

PomBase (https://www.pombase.org), the model organism database (MOD) for fission yeast, was recently awarded Global Core Biodata Resource (GCBR) status by the Global Biodata Coalition (GBC; https://globalbiodata.org/) after a rigorous selection process. In this MOD review, we present PomBase's continuing growth and improvement over the last 2 years. We describe these improvements in the context of the qualitative GCBR indicators related to scientific quality, comprehensivity, accelerating science, user stories, and collaborations with other biodata resources. This review also showcases the depth of existing connections both within the biocuration ecosystem and between PomBase and its user community.

FlyBase: updates to the Drosophila genes and genomes database

FlyBase (flybase.org) is a model organism database and knowledge base about Drosophila melanogaster, commonly known as the fruit fly. Researchers from around the world rely on the genetic, genomic, and functional information available in FlyBase, as well as its tools to view and interrogate these data. In this article, we describe the latest developments and updates to FlyBase. These include the introduction of single-cell RNA sequencing data, improved content and display of functional information, updated orthology pipelines, new chemical reports, and enhancements to our outreach resources.

CaveCrawler: an interactive analysis suite for cavefish bioinformatics

The growing use of genomics in diverse organisms provides the basis for identifying genomic and transcriptional differences across species and experimental conditions. Databases containing genomic and functional data have played critical roles in the development of numerous genetic models but most emerging models lack such databases. The Mexican tetra, Astyanax mexicanus exists as 2 morphs: surface-dwelling and cave-dwelling. There exist at least 30 cave populations, providing a system to study convergent evolution. We have generated a web-based analysis suite that integrates datasets from different studies to identify how gene transcription and genetic markers of selection differ between populations and across experimental contexts. Results of diverse studies can be analyzed in conjunction with other genetic data (e.g. Gene Ontology information), to enable biological inference from cross-study patterns and identify future avenues of research. Furthermore, the framework that we have built for A. mexicanus can be adapted for other emerging model systems.

Humanized yeast to model human biology, disease and evolution

For decades, budding yeast, a single-cellular eukaryote, has provided remarkable insights into human biology. Yeast and humans share several thousand genes despite morphological and cellular differences and over a billion years of separate evolution. These genes encode critical cellular processes, the failure of which in humans results in disease. Although recent developments in genome engineering of mammalian cells permit genetic assays in human cell lines, there is still a need to develop biological reagents to study human disease variants in a high-throughput manner. Many protein-coding human genes can successfully substitute for their yeast equivalents and sustain yeast growth, thus opening up doors for developing direct assays of human gene function in a tractable system referred to as 'humanized yeast'. Humanized yeast permits the discovery of new human biology by measuring human protein activity in a simplified organismal context. This Review summarizes recent developments showing how humanized yeast can directly assay human gene function and explore variant effects at scale. Thus, by extending the 'awesome power of yeast genetics' to study human biology, humanizing yeast reinforces the high relevance of evolutionarily distant model organisms to explore human gene evolution, function and disease.

Lord of the fruit flies: an interview with Hugo Bellen

During his remarkable career, Professor Hugo Bellen has innovated Drosophila genetics and forged a community driven toward diagnosis and treatment of rare diseases. He has advanced our understanding of nervous system development and neurodegeneration by exploring mechanisms and genetics through the latticed eyes of the common fruit fly. His lab, along with the labs of Shinya Yamamoto and Michael Wangler at Baylor College of Medicine and the Jan and Dan Duncan Neurological Research Institute of Texas Children's Hospital in Houston, also function as the Drosophila Core of the Model Organisms Screening Center (MOSC) of the Undiagnosed Diseases Network (UDN) and the Center for Precision Medicine Models. In this capacity, they facilitate the diagnosis of (ultra)rare human diseases and contribute to the development of treatments for these patients. Hugo is also the head of the Drosophila Gene Disruption Project supported by the National Institutes of Health (NIH) Office of Research Infrastructure Programs, and his lab channels substantial resources to the development of novel and sophisticated tools and technology that are then shared openly with the community via the Bloomington Drosophila Stock Center and the Drosophila Genomics Resource Center to propel research across the globe. Hugo has received an array of awards for his contributions to science and medicine, and he continues to be one of the most prominent figures in translational model organism research. In this interview, he discusses how his career progressed towards Drosophila genetics and highlights the accomplishments and challenges faced by the model organism community.

The power of Drosophila in modeling human disease mechanisms

Six years ago, DMM launched a subject collection called ‘Drosophila as a Disease Model’. This collection features Review-type articles and original research that highlight the power of Drosophila research in many aspects of human disease modeling. In the ensuing years, Drosophila research has further expanded to capitalize on genome editing, development of resources, and further interest in studying rare disease mechanisms. In the current issue of DMM, we again highlight the versatility, breadth, and scope of Drosophila research in human disease modeling and translational medicine. While many researchers have embraced the power of the fly, many more could still be encouraged to appreciate the strengths of Drosophila and how such research can integrate across species in a multi-pronged approach. Only when we truly acknowledge that all models contribute to our understanding of human biology, can we take advantage of the scope of current research endeavors.

Summary: This Editorial encourages us to embrace the power of the fly in studying human disease and highlights how Drosophila studies can be integrated with research in other species to further our understanding of human biology.