Lesack, K. J. | Search bioRxiv

bioRxiv2025

Genome structural variation in natural Caenorhabditis elegans populations

Structural variation, involving large alterations in chromosome structure, drives genetic diversification and the emergence of new phenotypes. These changes are widespread in natural populations and play an important role in adaptation and speciation. For many species, research has been limited to laboratory adapted strains and experimental evolution, which may not reflect the diversity of structural variants in the wild. Furthermore, technological limitations have proved to be a major barrier to accurate and comprehensive variant calling. In this study, we used PacBio sequencing data from 14 wild Caenorhabditis elegans strains to characterize structural variants in a natural population. With long-reads, we overcame limitations associated with short-read approaches and leveraged population-level data to further refine the accuracy of variant calls. We found that large, rapidly evolving gene families, such as GPCR, F-Box, and C-Type lectin, were prominent among the variants predicted to have phenotypic consequences. These results shed light on the significant role of structural variants in the evolution of Caenorhabditis elegans in its wild habitats and the limitations of treating N2 as the reference wild-type.

evolutionary biology↗

bioRxiv2018

Nomenclature Errors in Public 16S rRNA Gene Reference Databases

BackgroundTargeted gene surveys of the 16S rRNA gene have become a standard method for profiling the membership and biodiversity of microbial communities. These studies rely upon specialized databases that provide reference sequences and their corresponding taxonomic classifications, but few independent evaluations of the nomenclature used in the taxonomic classifications have been performed.\n\nResultsNomenclature data collected from the List of Prokaryotic names with Standing in Nomenclature, Prokaryotic Nomenclature Up-to-Date, and CyanoDB databases were used to validate the nomenclature contained in the taxonomic classifications in the Greengenes, RDP, and SILVA 16S rRNA gene reference databases. Between 82% and 97% of the genus annotations assigned to 16S rRNA gene reference sequences were deemed valid in the reference databases. Between 18% and 97% of the species annotations in Greengenes and SILVA were deemed valid. Misannotations included the use of metadata in place of taxonomic classifications, non-adherence to the binomial nomenclature, and sequences classified as eukaryote organelles or taxa.\n\nConclusionsThe misannotations identified in public 16S rRNA gene databases call into question the reliability of research made using these resources. As targeted gene surveys depend on high quality marker gene databases, imed nomenclature accuracy will be necessary.

microbiology↗