starbase: A Database and Toolkit for Exploration of Extremely Large Mobile Elements in Fungi

Abstract

Starships are a recently discovered superfamily of extremely large mobile genetic element (MGE)s in fungi that encode diverse gene sequences, many of unknown function. Starships are widespread throughout filamentous Ascomycetes (Pezizomycotina), but relatively little is known about their fine-grained distributions at lower taxonomic levels. As more and more Starships are discovered, it is increasingly important to more effectively catalog their gene contents and taxonomic distributions to better understand their contributions to fungal evolution. To address this, we developed starbase, a web server and comparative toolkit for exploring Starship diversity and hypothesis generation. The starbase database is constructed from Starships identified from existing studies, as well as an exhaustive de novo survey of Starship sequences within a set of 19 863 publicly available fungal genome assemblies. This database consists of 5 493 Starships, their associated nucleotide sequences, captain gene protein sequences, cargo gene annotations, and other metadata pertaining to the annotation and analysis of Starships in fungal genomes. As a resource, starbase provides new avenues for studying structural variation in fungal genomes. starbase provides several key features for the research community: a centralized repository of curated Starship annotations, a standardized accessioning system enabling consistent referencing of elements across studies, tools for searching existing sequences and classifying novel Starships based on established classification schemes, and a submission portal encouraging community contributions. As Starship identification becomes a routine component of fungal genome annotation, starbase provides a framework for organizing this growing body of data and facilitating comparative analyses across the expanding landscape of fungal genomic diversity.