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Science Papers Present Long-Lived Rockfish Genome Analysis, Arabidopsis Centromeres, Protein Complexes

By studying the genomes of multiple species of Pacific Ocean rockfish, which show extreme variation in lifespan ranging from 11 years to more than 200 years, a team led by scientists from the University of California, Berkeley, have uncovered new insights into the genetics of longevity. In the study, which appears in this week's Science, the researchers sequenced and de novo assembled the genomes of 102 individual rockfish representing 88 different rockfish species. With these data, they identified repeated signatures of positive selection in DNA repair pathways in long-lived taxa and 137 longevity-associated genes with both direct effects on lifespan, such as through insulin signaling, and indirect effects, including through size and environmental adaptations to depth. A genome-wide screen of structural variation, meanwhile, pointed to a specific gene family, the butyrophilins, that may play a role in modulating lifespan in rockfish. "Further, our results indicate that such life-history transitions themselves reshape patterns of genetic diversity," they write. "Long-lived rockfish species exhibit reduced genetic diversity in contrast to short-lived species, and the mutational spectrum of segregating genetic variation is also altered by life span." GenomeWeb has more on this, here.

Leveraging advances in sequencing technology and genome assembly, a University of Cambridge-led team has generated a reference genome for the Arabidopsis thaliana accession Columbia (Col-CEN). While the Arabidopsis genome was first sequenced in 2000, the centromeres, telomeres, and ribosomal DNA repeats have remained unassembled due to their high repetition and similarity. As reported in Science, by using long-read Oxford Nanopore Technologies sequencing, followed by polishing with Pacific Biosciences high-fidelity reads, the scientists were able to establish a Col-CEN reference assembly that wholly resolves all five Arabidopsis centromeres. "Together, our Col-CEN assembly reveals the genetic and epigenetic landscapes within the Arabidopsis centromeres," they write.

Using cutting-edge computational technologies, a team led by scientists from the University of Washington report in this week's Science more than 1,500 pairs of yeast proteins likely to interact, highlighting how computational advances can help further understanding of fundamental cellular processes. Protein-protein interactions play critical roles in biology, but the structures of many eukaryotic protein complexes are unknown and there are likely many interactions not yet identified. Taking advantage of the deep learning-based structure prediction methods RoseTTAFold and AlphaFold, the researchers screened through paired multiple sequence alignments for 8.3 million pairs of Saccharomyces cerevisiae proteins, identifying 1,505 likely to interact. Then then built structure models for 106 previously unidentified assemblies and 806 that have not been structurally characterized. "These complexes, which have as many as five subunits, play roles in almost all key processes in eukaryotic cells and provide broad insights into biological function," the study's authors write. "Our results herald a new era of structural biology in which computation plays a fundamental role in both interaction discovery and structure determination." GenomeWeb also covers this, here.

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