No abstract

For decades the soil nematode Caenorhabditis elegans has been an important model system for biology, but little is known about its natural ecology. Recently, C. elegans has become the focus of studies of innate immunity and several pathogens have been shown to cause lethal intestinal infections in C. elegans. However none of these pathogens has been shown to invade nematode intestinal cells, and no pathogen has been isolated from wild-caught C. elegans. Here we describe an intracellular pathogen isolated from wild-caught C. elegans that we show is a new species of microsporidia. Microsporidia comprise a large class of eukaryotic intracellular parasites that are medically and agriculturally important, but poorly understood. We show that microsporidian infection of the C. elegans intestine proceeds through distinct stages and is transmitted horizontally. Disruption of a conserved cytoskeletal structure in the intestine called the terminal web correlates with the release of microsporidian spores from infected cells, and appears to be part of a novel mechanism by which intracellular pathogens exit from infected cells. Unlike in bacterial intestinal infections, the p38 MAPK and insulin/insulin-like growth factor (IGF) signaling pathways do not appear to play substantial roles in resistance to microsporidian infection in C. elegans. We found microsporidia in multiple wild-caught isolates of Caenorhabditis nematodes from diverse geographic locations. These results indicate that microsporidia are common parasites of C. elegans in the wild. In addition, the interaction between C. elegans and its natural microsporidian parasites provides a system in which to dissect intracellular intestinal infection in vivo and insight into the diversity of pathogenic mechanisms used by intracellular microbes.

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.

Author contributions M.K. co-designed and implemented the overall strategy for the creation of the knock-in fly lines, designed and implemented the bioassays, the RT-qPCR experiments and the RMO analysis, performed statistical analyses and co-wrote the manuscript. S.C.G. designed and implemented the overall strategy for the creation of the knock-in fly lines, prepared the sequence data and metadata for the phylogenetic analyses, co-designed all other experiments, and co-wrote the manuscript. F.S. performed the structural modelling and docking site analyses. J.N.P. performed the phylogenetic, ancestral state and co-evolutionary analyses. K.I.V. conducted crosses, genotyping, and feeding experiments, and co-designed the qPCR experiments. J.M.A. and S.L.B. conducted crosses and genotyping, and feeding and sequestration experiments. A.P.H. performed the in vitro physiological experiments and sequestration analyses. T.M. conducted feeding experiments M.A. performed the RMO analysis with M.K., and conducted genotyping and feeding experiments. G.G. completed the RMO and ouabain dietary survival analyses. F.R. supervised the structural modelling and docking site analyses. S.D. oversaw and interpreted in vitro cell line analyses, helped to design the overall project and co-wrote the manuscript. A.A.A. helped to design the overall project, oversaw the in vitro physiological and sequestration experiments, and co-wrote the manuscript. N.K.W. led the overall collaboration, the project design and its integration, creation of fly lines and statistical analyses, and co-wrote the manuscript. Peer review information Nature thanks Joseph W. Thornton and the other, anonymous, reviewer(s) for their contribution to the peer review of this work.Online content Any methods, additional references, Nature Research reporting summaries, source data, extended data, supplementary information, acknowledgements, peer review information; details of author contributions and competing interests; and statements of data and code availability are available at