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Science Presents OpenCell Proteomic Map, Sequencing Analysis of Betta Fish Domestication

A study mapping the localization and interactions of human proteins, along with a web-based resource for analyzing and sharing the data, are presented in this week's Science. Sequencing the human genome has yielded the complete set of proteins that give rise to the human cell. Yet systematically characterizing how proteins organize within the cell to sustain its operation remains a key goal in the post-genomic era. To that end, investigators from the Chan Zuckerberg Biohub used a combination of high-throughput CRISPR-mediated genome engineering, confocal live-cell imaging, mass spectrometry, and computational technologies to create a proteomic map of human cellular architecture dubbed OpenCell. The resource, the scientists write, provides insights into the function of individual proteins and enables the identification of some general principles of human cellular organization such as how proteins that bind RNA form a separate subgroup defined by specific localization and interaction signatures. "We also show that the precise spatial distribution of a given protein is very strongly correlated with its cellular function, such that fine-grained molecular insights can be derived from the analysis of imaging data," they write. The researchers additionally built an interactive web interface for exploring their open-source dataset.

Combining population and quantitative genetic approaches, a team led by Columbia University researchers has uncovered new details about the domestication and phenotypic diversification of the Siamese fighting (betta) fish. Bettas have been selectively bred for fighting in Southeast Asia for centuries and, starting in the 20th century, have also been bred for ornamental purposes. This breeding history, along with betta's relatively small vertebrate genome, make the fish an appealing subject for evolutionary genetic studies of domestication. In this week's study, which appears in Science Advances, the investigators assembled the de novo genome of a wild Betta splendens — the species from which domestic fighting fish were mainly derived — and whole-genome sequenced 98 individuals across five closely related species. They find evidence of bidirectional hybridization between domesticated ornamental betta and other wild betta species. They also identify one specific gene as the main sex determination gene in ornamental betta, as well as strongly selected genes with large effects on color in specific parts of the body or on the shape of fins. "Our results provide molecular entry points for further study of the developmental and evolutionary bases of change in morphology and sex determination," the scientists write. "The genomic resources that we generated will also enable genetic studies into how centuries of artificial selection of betta for fighting purposes have shaped their aggression and other fighting-related traits."

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