Abstract. BacMap 3.0 (https://bacmap.ca) is a comprehensive, freely accessible resource integrating 23 524 bacterial and archaeal species, 32 866 genomes,

Study of 243 ancient genomes shows Roman rule changed Iberia's population far more than the Visigoths, Suebi and Alans did.

Pseudomonas spp. are common contributors to spoilage of refrigerated foods and can produce visible quality defects, including discoloration (1, 2). We isolated three pigmented Pseudomonas strains from...

Viral RNA genomes fold into networks of compact structures, so their RNA sequences do more than carry genetic code. Hann et al. review how viral RNA structures control viral gene expression, replicati...

Filamentous phages play important roles in molecular biology and bacterial pathogenesis. There is therefore great interest in the genomes of the phages, including M13 and Pf, which infect Escherichia coli and Pseudomonas aeruginosa , respectively. However, efficient methods for purifying single-stranded DNA (ssDNA) from filamentous phages are scarce and rely mainly on repurposed commercial kits developed for dsDNA. These kits yield variable amounts of ssDNA, varying considerably from one phage to another, their solutions are proprietary and troubleshooting, and customizing the protocol to improve purification is not possible. Here, we developed and optimized two protocols based on ssDNA binding to silica columns in the presence of guanidine hydrochloride and potassium iodide chaotropic salts, for filamentous phages M13KO7 and Pf4. The protocols achieved 60 to 100% recovery, equal to or higher than the Monarch Spin gDNA Extraction and DNeasy Blood and Tissue kits, with similar A260/280 and A260/230 ratios, intact DNA in agarose gels, and no detectable host genomic DNA by PCR. Recovery depended critically on the chaotropic salts and on ethanol, and did not increase at lower pH, consistent with a water-exclusion model in which hydrophobic interactions and hydrogen bonding dominate over electrostatic repulsion. Phage-specific differences in recovery indicate that optimization may be needed for some phages, which the fully customizable nature of these protocols facilitates. Comparing the virion ssDNA with the double-stranded replicative form (RF) revealed genome variants in both phages, including a shorter M13KO7 form lacking the kanamycin resistance-p15A insert, and illustrates the value of analyzing both RF and ssDNA forms to study filamentous phage biology. Implementing these protocols in routine filamentous phage workflows should facilitate their characterization and engineering. ### Competing Interest Statement The authors have declared no competing interest. Stanford Maternal and Child Health Research Institute, Postdoctoral Fellowship Cystic Fibrosis Research Institute (CFRI), Elizabeth Nash Memorial Fellowship National Institutes of Health, K08 AI190313, R01 HL148184-01, R01 AI12492093, R01 DC019965, K24 AI166718, P01AI1960471 Cystic Fibrosis Foundation, https://ror.org/00ax59295

Loss of biodiversity can have a hidden dimension—the cryptic erosion of genetic diversity even in the face of apparent species resilience. We quantified changes in genetic diversity by comparing histo...

Abstract. Coleoid cephalopods have convergently evolved many traits shared with vertebrates, including camera-type eyes, large brain-to-body size ratios, a