WormBase 2016: expanding to enable helminth genomic research

Howe, Kevin; Bolt, Bruce J.; Cain, Scott; Chan, Juancarlos; Chen, Wen J.; Davis, Paul A.; Done, James; Down, Thomas A.; Gao, Sibyl; Grove, Christian A.; Harris, Todd W.; Kishore, Ranjana; Lee, Raymond Y. N.; Lomax, Jane; Li, Yuling; Müller, Hans‐Michael; Nakamura, Cecilia; Nuin, Paulo; Paulini, M.; Raciti, Daniela; Schindelman, Gary; Stanley, Eleanor; Tuli, Mary Ann; Auken, Kimberly Van; Wang, Daniel; Wang, Xiaodong; Williams, Gary W.; Wright, Adam; Yook, Karen; Berriman, Matthew; Kersey, Paul J.; Schedl, Tim; Stein, Lincoln; Sternberg, Paul W.

doi:10.1093/nar/gkv1217

Cited by 320 publications

(367 citation statements)

References 42 publications

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“…High-throughput RNA-seq data were aligned to the T. muris reference genome models (WormBase WS255; http://parasite.wormbase.org; [31]) using the STAR transcriptome aligner [32]. Prior to downstream analysis, rRNA-like sequences were removed from the metatranscriptomic dataset using riboPicker-0.4.3 (http://ribopicker.sourceforge.net; [33]).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

107

145

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Whipworms are parasitic nematodes that live in the gut of more than 500 million people worldwide. Owing to the difficulty in obtaining parasite material, the mouse whipworm Trichuris muris has been extensively used as a model to study human whipworm infections. These nematodes secrete a multitude of compounds that interact with host tissues where they orchestrate a parasitic existence. Herein we provide the first comprehensive characterization of the excretory/secretory products of T. muris. We identify 148 proteins secreted by T. muris and show for the first time that the mouse whipworm secretes exosome-like extracellular vesicles (EVs) that can interact with host cells. We use an Optiprep® gradient to purify the EVs, highlighting the suitability of this method for purifying EVs secreted by a parasitic nematode. We also characterize the proteomic and genomic content of the EVs, identifying >350 proteins, 56 miRNAs (22 novel) and 475 full-length mRNA transcripts mapping to T. muris gene models. Many of the miRNAs putatively mapped to mouse genes are involved in regulation of inflammation, implying a role in parasite-driven immunomodulation. In addition, for the first time to our knowledge, colonic organoids have been used to demonstrate the internalization of parasite EVs by host cells. Understanding how parasites interact with their host is crucial to develop new control measures. This first characterization of the proteins and EVs secreted by T. muris provides important information on whipworm–host communication and forms the basis for future studies.

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Section: Methodsmentioning

confidence: 99%

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Eichenberger

Talukder

Field

et al. 2018

J of Extracellular Vesicle

107

145

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“…Genome sequences and annotation GFFs were downloaded from WormBase [25] and imported into a custom Ensembl database (version 84) [26]. Using the Ensembl Perl API, the canonical transcript from each proteincoding gene was identified and exon and intron statistics were calculated.…”

Section: Gene Structure Comparisonsmentioning

confidence: 99%

Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

et al. 2017

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Background: The genus Caenorhabditis has been central to our understanding of metazoan biology. The best-known species, Caenorhabditis elegans, is but one member of a genus with around 50 known species, and knowledge of these species will place the singular example of C. elegans in a rich phylogenetic context. How did the model come to be as it is today, and what are the dynamics of change in the genus?Results: As part of this effort to "put C. elegans in its place", we here describe the morphology and genome of Caenorhabditis monodelphis sp. n., previously known as Caenorhabditis sp. 1. Like many other Caenorhabditis, C. monodelphis sp. n. has a phoretic association with a transport host, in this case with the fungivorous beetle Cis castaneus. Using genomic data, we place C. monodelphis sp. n. as sister to all other Caenorhabditis for which genome data are available. Using this genome phylogeny, we reconstruct the stemspecies morphological pattern of Caenorhabditis. Conclusions:With the morphological and genomic description of C. monodelphis sp. n., another key species for evolutionary and developmental studies within Caenorhabditis becomes available. The most important characters are its early diverging position, unique morphology for the genus and its similarities with the hypothetical ancestor of Caenorhabditis.

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“…Many model organism databases, such as FlyBase, 8 WormBase, 21 and ZFIN, 10 are comprehensive and contain a monumental amount of data accumulated over numerous decades. 45 However, the extremely valuable information in these databases is not easily accessible by those outside the field.…”

Section: Discussionmentioning

confidence: 99%

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

Wang¹,

Al‐Ouran²,

Hu³

et al. 2017

The American Journal of Human Genetics

191

146

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One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format. To this end, we created MARRVEL (model organism aggregated resources for rare variant exploration). MARRVEL is a publicly available website that integrates information from six human genetic databases and seven model organism databases. For any given variant or gene, MARRVEL displays information from OMIM, ExAC, ClinVar, Geno2MP, DGV, and DECIPHER. Importantly, it curates model organism-specific databases to concurrently display a concise summary regarding the human gene homologs in budding and fission yeast, worm, fly, fish, mouse, and rat on a single webpage. Experiment-based information on tissue expression, protein subcellular localization, biological process, and molecular function for the human gene and homologs in the seven model organisms are arranged into a concise output. Hence, rather than visiting multiple separate databases for variant and gene analysis, users can obtain important information by searching once through MARRVEL. Altogether, MARRVEL dramatically improves efficiency and accessibility to data collection and facilitates analysis of human genes and variants by cross-disciplinary integration of 18 million records available in public databases to facilitate clinical diagnosis and basic research.

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WormBase 2016: expanding to enable helminth genomic research

Cited by 320 publications

References 42 publications

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Characterization of Trichuris muris secreted proteins and extracellular vesicles provides new insights into host–parasite communication

Caenorhabditis monodelphis sp. n.: defining the stem morphology and genomics of the genus Caenorhabditis

MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome

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