Caenorhabditis nomenclature

Genetic nomenclature allows the genetic features of an organism to be structured and described in a uniform and systematicway. Genetic features, including genes, variations (both natural and induced), and gene products, are assigned descriptorsthat inform on the nature of the feature. These nomenclature designations facilitate communication among researchers (in publications,presentations, and databases) to advance understanding of the biology of the genetic feature and the experimental utilizationof organisms that contain the genetic feature. The nomenclature system that is used for C. elegans was first employed by Sydney Brenner (1974) in his landmark description of the genetics of this model organism, and then substantially extended and modified in Horvitz et al., 1979. The gene, allele, and chromosome rearrangement nomenclature, described below, is an amalgamation of that from bacteria andyeast, with the rearrangement types from Drosophila. The nomenclature avoids standard words, subscripts, superscripts, and Greek letters and includes a hyphen (-) to separatethe gene name from gene number (distinct genes with similar phenotypes or molecular properties). As described by Jonathan Hodgkin, ‘the hyphen is about 1 mm in length in printed text and therefore symbolizes the 1 mm long worm’. These nomenclature propertiesmake C. elegans publications highly suitable for informatic text mining, as there is minimal ambiguity. From the founding of the CaenorhabditisGenetics Center (CGC) in 1979 until 1992, Don Riddle and Mark Edgley acted as the central repository for genetic nomenclature. Jonathan Hodgkin was nomenclature czar from 1992 through 2013; this was a pivotal period with the elucidation of the genome sequence of C. elegans, and later that of related nematodes, and the inception of WormBase. Thus, under the guidance of Hodgkin, the nomenclature system became a central feature of WormBase and the number and types of genetic features significantly expanded. The nomenclature system remains dynamic, with recentadditions including guidelines related to genome engineering, and continued reliance on the community for input. WormBase assigns specific identifying codes to each laboratory engaged in dedicated long-term genetic research on C. elegans. Each laboratory is assigned a laboratory/strain code for naming strains, and an allele code for naming genetic variation(e.g., mutations) and transgenes. These designations are assigned to the laboratory head/PI who is charged with supervisingtheir organization in laboratory databases and their associated biological reagents that are described on WormBase, in publications, and distributed to the scientific community on request. The laboratory/strain code is used: a) to identifythe originator of community-supplied information on WormBase, which, in addition to attribution, facilitates communicationbetween the community/curators and the originator if an issue related to the information should arise at a later date; andb) to provide a tracking code for activities at the CGC. The laboratory/strain designation consists of 2-3 uppercase letters while the allele designation has 1-3 lowercase letters.The final letter of a laboratory code should not be an “O” or an “I” so as not to be mistaken for the numbers “0” or “1” respectively.Additionally, allele designations should also not end with the letter “l” which could also be mistaken for the number “1.” These codes are listed at the CGC and in WormBase. Investigators generating strains, alleles, transgenes, and/or defining genes require these designations and should applyfor them at [email protected]. Information for several other nematode species, in addition to C. elegans, is curated at WormBase. All species are referred to by their Linnean binomial names (e.g,. Caenorhabditis elegans or C. elegans). Details of all the genomes available at WormBase and the degree of their curation can be found at www.wormbase.org/species/al

WormBase: A modern Model Organism Information Resource

WormBase (https://wormbase.org/) is a mature Model Organism Information Resource supporting researchers using the nematode Caenorhabditis elegans as a model system for studies across a broad range of basic biological processes. Toward this mission, WormBase efforts are arranged in three primary facets: curation, user interface and architecture. In this update, we describe progress in each of these three areas. In particular, we discuss the status of literature curation and recently added data, detail new features of the web interface and options for users wishing to conduct data mining workflows, and discuss our efforts to build a robust and scalable architecture by leveraging commercial cloud offerings. We conclude with a description of WormBase\u27s role as a founding member of the nascent Alliance of Genome Resources

Fog-2 and the evolution of self-fertile hermaphroditism in caenorhabditis

Somatic and germline sex determination pathways have diverged significantly in animals, making comparisons between taxa difficult. To overcome this difficulty, we compared the genes in the germline sex determination pathways of Caenorhabditis elegans and C. briggsae, two Caenorhabditis species with similar reproductive systems and sequenced genomes. We demonstrate that C. briggsae has orthologs of all known C. elegans sex determination genes with one exception: fog-2. Hermaphroditic nematodes are essentially females that produce sperm early in life, which they use for self fertilization. In C. elegans, this brief period of spermatogenesis requires FOG-2 and the RNA-binding protein GLD-1, which together repress translation of the tra-2 mRNA. FOG-2 is part of a large C. elegans FOG-2-related protein family defined by the presence of an F-box and Duf38/FOG-2 homogy domain. A fog-2-related gene family is also present in C. briggsae, however, the branch containing fog-2 appears to have arisen relatively recently in C. elegans, post-speciation. The C-terminus of FOG-2 is rapidly evolving, is required for GLD-1 interaction, and is likely critical for the role of FOG-2 in sex determination. In addition, C. briggsae gld-1 appears to play the opposite role in sex determination (promoting the female fate) while maintaining conserved roles in meiotic progression during oogenesis. Our data indicate that the regulation of the hermaphrodite germline sex determination pathway at the level of FOG-2/GLD-1/tra-2 mRNA is fundamentally different between C. elegans and C. briggsae, providing functional evidence in support of the independent evolution of self-fertile hermaphroditism. We speculate on the convergent evolution of hermaphroditism in Caenorhabditis based on the plasticity of the C. elegans germline sex determination cascade, in which multiple mutant paths yield self fertility

RNA-binding proteins

The C. elegans genome encodes many RNA-binding proteins (RBPs) with diverse functions in development, indicative of extensive layers of post-transcriptional control of RNA metabolism. A number of C. elegans RBPs have been identified by forward or reverse genetics. They tend to display tissue-specific mutant phenotypes, which underscore their functional importance. In addition, several RBPs that bind regulatory sequences in the 3'untranslated regions of mRNAs have been identified molecularly. Most C. elegans RBPs are conserved throughout evolution, suggesting that their study in C. elegans may uncover new conserved biological functions. In this review, we primarily discuss RBPs that are associated with well-characterized mutant phenotypes in the germ line, the early embryo, or in somatic tissues. We also discuss the identification of RNA targets of RBPs, which is an important first step to understand how an RBP controls C. elegans development. It is likely that most RBPs regulate multiple RNA targets. Once multiple RNA targets are identified, specific features that distinguish target from non-target RNAs and the type(s) of RNA metabolism that each RBP controls can be determined. Furthermore, one can determine whether the RBP regulates all targets by the same mechanism or different targets by distinct mechanisms. Such studies will provide insights into how RBPs exert coordinate control of their RNA targets, thereby affecting development in a concerted fashion

Micropublication: incentivizing community curation and placing unpublished data into the public domain

Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery

Caenorhabditis elegans glp-4 encodes a valyl aminoacyl tRNA synthetase

Germline stem cell proliferation is necessary to populate the germline with sufficient numbers of cells for gametogenesis and for signaling the soma to control organismal properties such as aging. The Caenorhabditis elegans gene glp-4 was identified by the temperature-sensitive allele bn2 where mutants raised at the restrictive temperature produce adults that are essentially germ cell deficient, containing only a small number of stem cells arrested in the mitotic cycle but otherwise have a morphologically normal soma. We determined that glp-4 encodes a valyl aminoacyl transfer RNA synthetase (VARS-2) and that the probable null phenotype is early larval lethality. Phenotypic analysis indicates glp-4(bn2ts) is partial loss of function in the soma. Structural modeling suggests that bn2 Gly296Asp results in partial loss of function by a novel mechanism: aspartate 296 in the editing pocket induces inappropriate deacylation of correctly charged Val-tRNA(val). Intragenic suppressor mutations are predicted to displace aspartate 296 so that it is less able to catalyze inappropriate deacylation. Thus glp-4(bn2ts) likely causes reduced protein translation due to decreased levels of Val-tRNA(val). The germline, as a reproductive preservation mechanism during unfavorable conditions, signals the soma for organismal aging, stress and pathogen resistance. glp-4(bn2ts) mutants are widely used to generate germline deficient mutants for organismal studies, under the assumption that the soma is unaffected. As reduced translation has also been demonstrated to alter organismal properties, it is unclear whether changes in aging, stress resistance, etc. observed in glp-4(bn2ts) mutants are the result of germline deficiency or reduced translation