Holm, J. | Search bioRxiv

bioRxiv2026

Experimental breeding reveals mating patterns and F1 phenotypic diversification in the cosmopolitan diatom Cylindrotheca

Diatom mating activity contributes to their enormous phenotypic and genetic diversity, yet little is known about patterns in diatom reproductive compatibility across genetically diverse strains, nor the effects on offspring phenotypes that may confer adaptive evolution, niche partitioning, or trait improvement. Here a panel of 38 Arctic Cylindrotheca sp. isolates were crossed pairwise to detect mating compatibility. Positive mating patterns were identified in multiple clades, including amongst crosses of different parental rbcL genotypes. F1 isolated from three different crosses presented phenotypic variation in growth rate, plastid traits, and associated photo-physiological responses to blue and green actinic light. Offspring gliding speed and behaviour also varied, providing insights into complex motility traits that link cell morphology, bioenergetics and sensory adaptation with emergent movement patterns. Exploratory analysis of the F1 trait landscape identified a varaible mixture of individual-level and cross-dependent effects, including substantial variation in growth rate between individuals and strong effects of different crosses on morphology and motility. Experimental diatom breeding may offer a unique strategy to study ocean protist evolution and phenotypic diversification and could complement other biotechnological innovations to enhance cultivation yields and crop resilience in mass cultivation.

microbiology↗

bioRxiv2019

VIRGO, a comprehensive non-redundant gene catalog, reveals extensive within community intraspecies diversity in the human vagina

BackgroundAnalysis of metagenomic and metatranscriptomic data is complicated and typically requires extensive computational resources. Leveraging a curated reference database of genes encoded by members of the target microbiome can make these analyses more tractable. Unfortunately, there is no such reference database available for the vaginal microbiome.\n\nResultsIn this study, we assembled a comprehensive human vaginal non-redundant gene catalog (VIRGO) from 264 vaginal metagenomes and 416 genomes of urogenital bacterial isolates. VIRGO includes 0.95 million non-redundant genes compiled from a total of 5.5 million genes belonging to 318 unique bacterial species. We show that VIRGO covers more than 95% of the vaginal bacterial gene content in metagenomes from North American, African, and Chinese women. The gene catalog was extensively functionally annotated from 17 diverse protein databases, and importantly taxonomy was assigned through in silico binning of genes derived from metagenomic assemblies. To further enable focused analyses of individual genes and proteins, we also clustered the non-redundant genes into vaginal orthologous groups (VOG). The gene-centric design of VIRGO and VOG provides an easily accessible tool to comprehensively characterize the structure and function of vaginal metagenome and metatranscriptome datasets. To highlight the utility of VIRGO, we analyzed 1,507 additional vaginal metagenomes, uncovering an as of yet undetected high degree of intraspecies diversity within and across vaginal microbiota.\n\nConclusionsVIRGO offers a convenient reference database and toolkit that will facilitate a more in-depth understanding of the role of vaginal microorganisms in womens health and reproductive outcomes.

genomics↗