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“Fish-out-of-water” offer ecologists and evolutionary biologists ideal opportunities to study the evolution of stress resistance in vertebrate species. Annual killifishes (Cyprinodontiformes: Aplocheiloidei) constitute one of the most intriguing systems to study fish-out-of-water. “Annual” fishes possess a suite of complex and key features that include diapause stages and desiccation resistance, allowing them to complete their life cycle in seasonal bodies of water. Embryos of some non-annual killifishes have been shown to exhibit pre-hatching delays or symptoms of dormancy (similar to diapause), therefore, these species may represent an intermediate phenotype in the evolution of an annual lifestyle. The non-annual killifish Aplocheilus lineatus undergoes such hatching delay during aerial incubation. We use this species to study gene expression differences among water-incubated and aerially-incubated embryos. Differentially expressed genes are characterized and compared with expression patterns during diapause in annual species and with other developmental stages in non-annual killifishes. The annotation of 560 differentially expressed transcripts provides insight into how delayed-hatching embryos of Aplocheilus lineatus react to aerial incubation and suggest that delayed hatching is a phenomenon distinct from the diapause stages of related annual species. Similar patterns of gene expression are shared among Aplocheilus and other egg stranding and amphibious fishes.

A personalized approach based on a patient's or pathogen’s unique genomic sequence is the foundation of precision medicine. Genomic findings must be robust and reproducible, and experimental data capture should adhere to findable, accessible, interoperable, and reusable (FAIR) guiding principles. Moreover, effective precision medicine requires standardized reporting that extends beyond wet-lab procedures to computational methods. The BioCompute framework (https://w3id.org/biocompute/1.3.0) enables standardized reporting of genomic sequence data provenance, including provenance domain, usability domain, execution domain, verification kit, and error domain. This framework facilitates communication and promotes interoperability. Bioinformatics computation instances that employ the BioCompute framework are easily relayed, repeated if needed, and compared by scientists, regulators, test developers, and clinicians. Easing the burden of performing the aforementioned tasks greatly extends the range of practical application. Large clinical trials, precision medicine, and regulatory submissions require a set of agreed upon standards that ensures efficient communication and documentation of genomic analyses. The BioCompute paradigm and the resulting BioCompute Objects (BCOs) offer that standard and are freely accessible as a GitHub organization (https://github.com/biocompute-objects) following the “Open-Stand.org principles for collaborative open standards development.” With high-throughput sequencing (HTS) studies communicated using a BCO, regulatory agencies (e.g., Food and Drug Administration [FDA]), diagnostic test developers, researchers, and clinicians can expand collaboration to drive innovation in precision medicine, potentially decreasing the time and cost associated with next-generation sequencing workflow exchange, reporting, and regulatory reviews., This Community Page article presents a communication standard for the provenance of high-throughput sequencing data; a BioCompute Object (BCO) can serve as a history of what was computed, be used as part of a validation process, or provide clarity and transparency of an experimental process to collaborators.