Abstract
Over 100 years of studies in Drosophila melanogaster and related species in the genus Drosophila have facilitated key discoveries in genetics, genomics, and evolution. While high-quality genome assemblies exist for several species in this group, they only encompass a small fraction of the genus. Recent advances in long-read sequencing allow high-quality genome assemblies for tens or even hundreds of species to be efficiently generated. Here, we utilize Oxford Nanopore sequencing to build an open community resource of genome assemblies for 101 lines of 93 drosophilid species encompassing 14 species groups and 35 sub-groups. The genomes are highly contiguous and complete, with an average contig N50 of 10.5 Mb and greater than 97% BUSCO completeness in 97/101 assemblies. We show that Nanopore-based assemblies are highly accurate in coding regions, particularly with respect to coding insertions and deletions. These assemblies, along with a detailed laboratory protocol and assembly pipelines, are released as a public resource and will serve as a starting point for addressing broad questions of genetics, ecology, and evolution at the scale of hundreds of species.
Highlights
The rise of long-read sequencing alongside the continuously decreasing costs of next-generation sequencing have served to greatly democratize the process of genome assembly, making it feasible to assemble high-quality genomes at a previously unthinkable scale
The genomic tractability that made drosophilids attractive for this work has led to their continued widespread use as model organisms in the genomic era: the whole-genome sequencing of 12 Drosophila species (Clark et al, 2007) and the characterization of functional elements in Drosophila genomes (Roy et al, 2010) are prominent milestones in the history of modern genomics
The sequenced species originate from mainland and island locations in North America, Europe, Africa, and Asia; are distributed from northern (e.g. D. tristis, D. littoralis) to equatorial (e.g. D. bocqueti) latitudes; represent two independent transitions to leafmining herbivory (Scaptomyza and Lordiphosa); and for some species, like the pest Zaprionus indianus, represent reproductively isolated populations taken from throughout the range
Summary
The rise of long-read sequencing alongside the continuously decreasing costs of next-generation sequencing have served to greatly democratize the process of genome assembly, making it feasible to assemble high-quality genomes at a previously unthinkable scale. In addition to establishing new standards for modern large-scale genomics projects and opening avenues for genomic research that were previously only feasible in model organisms across a multitude of species, these projects are creating an opportunity to study genetic variation and address fundamental biological questions at a scope that was not possible before. As a premier model organism for genetic and biological research since the foundational work of Morgan and colleagues, D. melanogaster was, after C. elegans, the second metazoan organism to undergo whole-genome sequencing (Adams et al, 2000). The genomic tractability that made drosophilids attractive for this work has led to their continued widespread use as model organisms in the genomic era: the whole-genome sequencing of 12 Drosophila species (Clark et al, 2007) and the characterization of functional elements in Drosophila genomes (Roy et al, 2010) are prominent milestones in the history of modern genomics
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