Consortium Wormbase et al. (2000) West Coast Worm Meeting "From ACeDB to a more complete and usable database"

Consortium Wormbase, Foltz NL, Schwarz EM, Sternberg PW

[West Coast Worm Meeting, 2000]

We briefly describe the current status and plans for WormBase, initially an extension of the existing ACeDB database with a new user interface. The WormBase consortium includes the team that developed ACeDB (Richard Durbin and colleagues at the Sanger Centre; Jean Thierry-Mieg and colleagues at Montpellier); Lincoln Stein and colleagues at Cold Spring Harbor, who developed the current web interface for WormBase; and John Spieth and colleagues at the Genome Sequencing Center at Washington University, who along with the Sanger Centre team, continue to annotate the genomic sequence. The Caltech group will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level, and gene interactions. Data will be extracted from the literature, as well as by community submission. We look forward to providing the C. elegans and broader research community easy access to vast quantities of high quality data on C. elegans. Also, we welcome your suggestions and criticism at any time. WormBase can be accessed at www.wormbase.org.

Sheldon J McKay et al. (2005) International Worm Meeting "Genome organization and colinearity in three Caenorhabditis species"

Sheldon J McKay, Lincoln D Stein

[International Worm Meeting, 2005]

C. elegans and C. briggsae are morphologically similar but their genomes have had about 100 million years to diverge. Examples of ways in which the two genomes have diverged include not only nucleotide substitutions but also species-specific expansion of gene families and many inter- and intra-chromosomal rearrangements (1). In addition to coding DNA and other functional sequences, higher order chromosome structure is also under selective constraints, for example against loss of genetic material due to non-reciprocal chromosome rearrangements. Conservation of regions of colinearity between divergent genomes suggests that gene order is also important. A striking example of this is the high degree inter-species conservation of gene order and composition of operons. We are building on the previously described comparison of the C. elegans and C. briggsae genomes using a global analysis of conservation of syntenic blocks in the genomes of these two species as well as that of C. remanei. The foundation of these comparisons is sequence similarity-based genome alignments performed by WABA(2) and blastz(3). Although conservation at the nucleotide sequence level is helpful in understanding genome evolution, global application of DNA sequence alignments in divergent genomes can be confounded by multiple rearrangements affecting the same region of the chromosome. Disruption in alignable sequences caused by a complex history of local rearrangements can mask larger blocks of colinearity that may be functionally significant. To identify such regions in these three species and, hopefully, unravel some of the complexity of nested chromosome rearrangements, we are applying a method based on the dynamic programming algorithm described in Stein et al. (1) and comparing it to the approach developed by Kent et al. (4) for the mouse and human genomes. We will discuss our findings in relation to the existing body of knowledge on C. elegans and C. briggsae genome organization and the impact of adding an additional species on our understanding of Caenorhabditis genome evolution. 1. Stein, L. D. et al., PLoS Biology 1:166-192 2. Kent, W. J. and A. M. Zahler, Genome Res 10:1115-1125 3. Schwartz, S. et al., Genome Res 13:103-107 4. Kent, W. J. et al., PNAS 100:11484-11489

Shakes, Diane et al. (2009) International Worm Meeting "EMB-1 is a novel protein involved in the metaphase-to-anaphase transition."

Golden, Andy, Shakes, Diane

[International Worm Meeting, 2009]

The Anaphase Promoting Complex (APC) is a multi-subunit E3 ubiquitin ligase that promotes the metaphase-to-anaphase transition during meiotic and mitotic divisions. Temperature-sensitive (ts) mutants in mat-1, mat-2, mat-3, emb-27, and emb-30 arrest as 1-cell embryos, stuck in metaphase of meiosis I. These five genes code for five subunits of the APC. The ts alleles of emb-1 have grabbed our attention because their arrest phenotype is indistinguishable from the APC mutants. Furthermore, genetic doubles constructed between emb-1(hc62) and the APC mutants cannot be maintained at the permissive temperature, a common feature of any APC double mutant. Additionally, suppressors that suppress the APC mutants (Stein et al., 2007) also suppress emb-1. What is EMB-1 you may ask? We mapped emb-1 to a tiny interval on LG III and used RNAi to phenocopy the 1-cell arrest phenotype. Rescue and sequencing confirmed that emb-1 codes for a novel protein with no known homologies outside of Caenorhabditis species. Localization studies are underway. We propose that EMB-1 is a novel subunit or regulator of the APC in C. elegans.

Bhaskar Reddy Gavinolla et al. (2007) International Worm Meeting "Interactions between the microtubule severing protein MEI-2 and spindle checkpoints."

Bhaskar Reddy Gavinolla, Paul E. Mains

[International Worm Meeting, 2007]

The spindle checkpoint protein, SAN-1/MDF-3 is expressed on mitotic centromeres. During anoxia, mutants fail to arrest the cell cycle, leading to chromosome mis-segregation and reduced viability (Nystul et. al 2003). Checkpoint proteins arrest the cell cycle by inhibiting the Anaphase Promoting Complex (APC) and san-1/mdf-3 mutants suppress APC mutants (Stein et al. 2007). We have uncovered a possible link between the microtubule severing complex MEI-1/MEI-2 and the meiotic spindle checkpoint. Like SAN-1/MDF-3, MEI-1 and MEI-2 localize to chromatin and genetically interact with APC mutants. Furthermore, yeast two hybrid data (Li et al. 2004) shows that MEI-2 and SAN-1 interact physically. Both the similar expression patterns and the yeast two-hybrid binding suggested possible genetic interaction between them, so we made double mutants of san-1 and mei-2. This resulted in increased lethality, low brood sizes and spontaneous males, indications of meiotic failure. While enhancement of mei-2 spindle formation defects might be expected by the presence of a compromised spindle checkpoint, the physical interaction and colocalization might indicate a more specific role for MEI-1/MEI-2 in monitoring spindle quality.

Nansheng Chen et al. (2005) International Worm Meeting "Conservation and Functional Significance of Overlapping Genes in Caenorhabditis elegan"

Nansheng Chen, Lincoln Stein

[International Worm Meeting, 2005]

We have systematically examined the overlapping genes in the Caenorhabditis elegans genome. There exist over one thousand such gene pairs in the entire C. elegans genome and can be subdivided into six major categories based on the overlap topology. We demonstrate that some categories of overlapping genes are bipolarized in terms of gene evolution. Some types of overlapping genes are strongly and significantly more conserved than the genome as a whole when compared to Caenorhabditis briggsae, a nematode that split from C. elegans about 100 million years ago (1), while other types of overlapping genes, the nested genes that reside within introns of other genes in particular, are significantly less conserved compared with other genes in the genome. We have also found that although overlapping gene pairs tend not to share common functional motifs, they are enriched with essential genes and genes that cause various defined phenotypes revealed by RNAi trials, indicating the functional significance of these genes. Tissue-specific SAGE library datasets analysis suggests that the flanking genes and their corresponding nested genes are not as strongly positively correlated in gene expression pattern as tandem gene pairs, suggesting that the flanking / nested gene pair arrangement interferes with coexpression among the members of the gene pairs. 1. L. D. Stein et al., PLoS Biol 1, E45 (Nov, 2003).

Scott E. Baird et al. (2007) International Worm Meeting "Available genetic and genomic resources for C. briggsae."

Daniel C. Koboldt, Raymond D. Miller, Bhagwati P. Gupta, Helen M. Chamberlin, Scott E. Baird, Eric S. Haag

[International Worm Meeting, 2007]

The draft genomic assembly of C. briggsae (Stein et al., 2003) has enabled detailed comparisons of specific gene sequences from C. elegans with a relative. However, C. briggsae has characteristics suggesting that more extensive comparisons of it with C. elegans are useful and further, that it is a useful model organism in its own right. We report here a number of recent accomplishments that will further facilitate research in C. briggsae. 1) A SNP-based genetic map of 6 chromosomes that links most of the draft sequence has been developed from recombinant inbred lines. 2) Over 24,000 SNPs have been identified from mapping strain HK104. 3). Insertion/deletion events useful for mapping have been identified including >7,000 that are short (<50 bp) and >600 candidates that are long (>50 bp). 4). A set of 50 phenotypic mutants are in various stages of localization to chromosomes. 5). A new set of 181 recombinant inbred lines useful for quantitative genetics has been developed. 6). New information on C. briggsae is available at http://www.wormbase.org and http://snp.wustl.edu. C. briggsae harbors considerable genetic diversity with a SNP detected on average every 115 bp between the canonical strain AF16 and the mapping strain HK104. C. briggsae is now a very attractive research model organism for forward genetics and the genetics of quantitative traits.

Haag, E.S. et al. (2019) International Worm Meeting "Evolution of sex ratio through gene loss."

Haag, E.S., Yin, D.

[International Worm Meeting, 2019]

The maintenance of males at intermediate frequencies is an important evolutionary problem. Several species of Caenorhabditis nematodes have evolved the androdioecious mating system, where selfing hermaphrodites and males coexist. They reproduce mostly through self-fertilization, but can also outcross. While selfing produces XX hermaphrodites, cross-fertilization produces 50% XO male progeny. Thus, male mating success dictates the sex ratio [1]. Here, we focus on the contribution of the male secreted short (mss) gene family to male mating success, sex ratio, and population growth. The mss family is essential for full sperm competitiveness in gonochoristic species, but has been lost in parallel in androdioecious species [2]. Using a transgene to restore mss function to the androdioecious C. briggsae, we examined how mating system and population subdivision influence the fitness of the mss+ genotype. Consistent with theoretical expectations, mss+ is sufficient to increase male frequency and depress population growth in genetically homogenous androdioecious populations. When mss+ and mss-null (i.e. wild-type) genotypes compete, mss+ is positively selected in both mixed-mating and strictly outcrossing situations, though more strongly in the latter. Thus, while sexual mode alone affects the fitness of mss+, it is insufficient to explain its parallel loss. We propose that the lack of inbreeding depression [3] and the strong subdivision that characterize natural Caenorhabditis populations [4] impose selection on sex ratio that makes loss of mss adaptive. By reducing, but not completely eliminating outcrossing, loss of the mss genes tunes the sex ratio to its new optimum after self-fertility is established. 1. Stewart AD, Phillips PC (2002) Genetics 160: 975 2. Yin et al. (2018) Science 359: 55 3. Dolgin et al. (2007) Evolution 61: 1339 4. Kiontke KC, et al. (2011) BMC Evol Biol 11: 339

Chu, Jeffrey Shih Chieh et al. (2009) International Worm Meeting "Reannotating the C. briggsae genome using genBlastG, a new homology-based gene finder."

Wang, Ke, Chen, Nansheng, She, Rong, Chu, Jeffrey Shih Chieh

[International Worm Meeting, 2009]

Since the publication of the C. briggsae genome annotation in 2003 [1], not much improvement has been done, although accumulating evidence suggests that many gene models are inaccurately predicted or missing. In this project, we have reannotated the C. briggsae genome, exploiting the much improved C. elegans genome annotation (using WS195, compared to WS77 annotation used for the original C. briggsae annotation), as well as a new homology-based gene finder we have developed, genBlastG. genBlastG builds on our recently published program genBlastA [2] and takes as input a query protein sequences and a genome sequence that will be annotated to produce all homologous gene models. Our analysis suggests that genBlastA outperforms GeneWise in both processing time (on average genBlastG runs ~50 times faster than GeneWise) and accuracy. We applied genBlastG to reannotate the C. briggsae genome. Our preliminary results from genBlastG produced 16,954 homologous models with the majority (11,235) matching well with the current WormBase annotation. However, a significant number (4,828) of genBlastG models exhibit better percent identity (PID) to the query protein sequence, the C. elegans query sequences. Thus, genBlastG models shows better homology to C. elegans models for many genes. In addition to better homology, our predictions also points out 261 WormBase models that should be split and 298 pairs of models should be merged. As an example of a model that should be merged, we found that CBG14800 and CBG14801 may actually be one gene that''s orthologous to C54G7.3a. CBG14801 may only represent the shorter isoform that''s orthologous to C54G7.3b. As an example of a model that should be split, we found that CBG00366 consists of orthologs from ZK550.3 and ZK550.4. In this presentation, I will summarize all improvement suggested by genBlastG. genBlastG will also be applied to predict gene models in other Caenorhabditis species. 1.Stein, L.D., et al., (2003). The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1: E45. 2.She, R., et al., (2009). GenBlastA: enabling BLAST to identify homologous gene sequences. Genome Res 19: 143-9.

Gill, R. et al. (2019) International Worm Meeting "Identifying biogenesis mechanisms for discrete subpopulations of extracellular vesicles."

Tanis, J., Gill, R., Touroutine, D., Clupper, M.

[International Worm Meeting, 2019]

Extracellular vesicles (EVs) are membrane wrapped structures containing proteins, RNAs, lipids, and metabolites that are released from most if not all cell types to mediate intercellular communication in physiological and pathological conditions. EVs fall into subclasses based on their mode of biogenesis. Exosomes are released following fusion of multivesicular bodies (MVBs) with the plasma membrane, while microvesicles form directly from plasma membrane budding. Our goal is to use C. elegans to identify proteins required for EV biogenesis in vivo. EVs are released from the cilia of the male specific cephalic male (CEM) neurons in the head and hook B type (HOB) and bilateral ray B type neurons (RnB) in the tail. These EVs are likely microvesicles as there is no evidence of MVBs in these neurons1. We discovered that the ion channel CLHM-1 is cargo in EVs released from C. elegans ciliated male sensory neurons by performing high resolution imaging of animals expressing functional GFP-tagged CLHM-1 at endogenous levels. Remarkably, when we co-expressed tdTomato-tagged CLHM-1 with GFP-tagged PKD-2, a known EV cargo protein expressed in the same neurons1, we rarely observed colocalization of the fluorescent proteins in vesicles, suggesting that CLHM-1 and PKD-2 are in discrete EV subpopulations. We are using the power of genetics to manipulate candidate EV biogenesis pathways to identify factors required for release of CLHM-1 containing EVs. Lipid asymmetry between the inner and outer leaflets of the plasma membrane induces curvature which could drive microvesicle release. Type IV-ATPase flippases translocate phospholipids from the outer to the inner leaflet to maintain bilayer asymmetry, while scramblases disrupt membrane asymmetry. We are determining if the flippases TAT-1, TAT-3, and TAT-6 as well as the scramblases ANOH-1 and SCRM-4 play a role in the biogenesis of one or both fluorescently marked EV subpopulations derived from male ciliated neurons. 1. Wang J, Silva M, Haas LA, Morsci NS, Nguyen KC, Hall DH, Barr MM. (2014) C. elegans ciliated sensory neurons release extracellular vesicles that function in animal communication. Curr Biol. 24(5):519-25.

Consortium Wormbase (2000) Worm Breeder's Gazette "Update on the C. elegans database WormBase"

Consortium Wormbase

[Worm Breeder's Gazette, 2000]

WormBase (www.wormbase.org) is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and some related nematodes. WormBase builds upon the existing ACeDB database of the C. elegans genome by providing curation from the literature, an expanded range of content and a user friendly web interface. The team that developed and maintained ACeDB (Richard Durbin, Jean Thierry-Mieg) remains an important part of WormBase. Lincoln Stein and colleagues at Cold Spring Harbor are leading the effort to develop the user interface, including visualization tools for the genome and genetic map. Teams at Sanger Centre (led by Richard Durbin) and the Genome Sequencing Center at Washington University, St. Louis (led by John Spieth) continue to curate the genomic sequence. Jean and Danielle Thierry-Mieg at NCBI spearhead importation of large-scale data sets from other projects. Paul Sternberg and colleagues at Caltech will curate new data including cell function in development, behavior and physiology, gene expression at a cellular level; and gene interactions. Paul Sternberg assumes overall responsibility for WormBase, and is delighted to hear feedback of any sort. WormBase has recently received major funding from the National Human Genome Research Institute at the US National Institutes of Health, and also receives support from the National Library of Medicine/NCBI and the British Medical Research Council. WormBase is an expansion of existing efforts, and as such continues to need you help and feedback. Even with the increased scope and funding, all past contributors to ACeDB remain involved. The Caenorhabditis Genetics Center (Jonathan Hodgkin and Sylvia Martinelli) collaborate with WormBase to curate the genetic map and related topics. Ian Hope and colleagues continue to supply expression data to WormBase. Leon Avery will continue his superb website and serves as one advisor to WormBase. While the major means of access to WormBase is via the world wide web, downloadable versions of WormBase as well as the acedb software engine will continue to be available.