Gysi, Stephan et al. (2009) International Worm Meeting "A screen for genes paralleling the function of HSPGs during C. elegans nervous system development."

Rhiner, Christa, Reh, Lucia, Hengartner, Michael, Gysi, Stephan, Egli, Ronald

[International Worm Meeting, 2009]

During nervous system development axons navigate through the extracellular matrix (ECM) to their target. Axons obtain the information where to grow from guidance cues located in the ECM or on cells neighbouring the growth path of the axon. A number of these guidance cues have been characterized in the past. However, there is increasing evidence that there are other molecules around that fine-tune the response of the axon to the various cues it senses. Heparan sulfate proteoglycans (HSPGs) are proteins that carry long sugar side chains. HSPGs have been shown to interact with a wide variety of morphogenes in vertebrates and invertebrates. We have previously described the role played by the HSPG Syndecan (SDN-1) during nervous system development in C. elegans. It is, however, still unknown through what mechanism SDN-1 exerts its function. Furthermore there is genetic evidence that there is at least one other HSPG core protein acting in parallel to SDN-1. With the aim to find genetic interactors of SDN-1, we performed forward genetic screens. We have screened about 20''000 genomes and isolated 10 candidate mutations. FLP and SNP mapping revealed that they map to 8 different intervals. Candidate op481 is mapping to the middle of chromosome three to an interval not containing any previously described axon guidance gene. Sequencing revealed that op481 carries a premature stop codon in the gene zfp-1. We will show a first characterization of the function of zfp-1 in axon guidance. Additionally epistasis analysis of the different candidates will show whether we identified multiple parallel signalling pathways.

Moya, Nicolas D. et al. (2021) International Worm Meeting "Improved reference genomes for Caenorhabditis briggsae"

Chitrakar, Rojin, Stevens, Lewis, Baugh, L. Ryan, Moya, Nicolas D., Walhout, Marian, Tanny, Robyn E., Dekker, Job, Na, Huimin, Andersen, Erik C.

[International Worm Meeting, 2021]

Decades of research have led to the development of comprehensive genome resources that have been essential to study the Caenorhabditis elegans species. In parallel, the emergence of Caenorhabditis briggsae as a model system has been useful to make interspecies comparisons. Despite the importance of C. briggsae as a model, its genome resources have not been developed to the same extent as C. elegans. The current genome of C. briggsae reference strain AF16 contains thousands of unresolved gaps and numerous mis-assemblies. Because of these issues, C. briggsae gene models remain incomplete and have numerous structural errors in protein-coding genes. We sought to exploit the latest sequencing technologies and computational tools to provide the highest quality C. briggsae genome resources to date. First, we generated high-quality genome assemblies for two strains of C. briggsae: QX1410 (a "tropical" strain isolated in Saint Lucia that is closely related to AF16) and VX34 (a divergent strain isolated in China). These genome assemblies incorporate high coverage Oxford Nanopore PromethION long reads and chromosome conformation capture (Hi-C) data. Second, we genotyped 99 recombinant inbred lines generated from reciprocal crosses between QX1410 and VX34. Using these data, we produced a high-quality recombination map that validated the placement of scaffolds after genome assembly. Third, we sequenced the transcriptomes of each strain to high coverage using Pacific Biosciences SMRT and Illumina platforms. We developed a computational pipeline that leverages long and short RNA reads to generate a genome annotation for each strain. These new genome annotations have improved accuracy and completeness relative to the AF16 genome. Fourth, our research group currently maintains over 1,600 C. briggsae wild strains, comprising the largest collection worldwide. We sequenced the genomes of this entire collection to high coverage using the Illumina platform. We mapped the sequences of all wild strains to the QX1410 genome to call single nucleotide variants across the entire population. These high-quality genome resources will facilitate new avenues of research, including quantitative and population genetic studies of C. briggsae, and enable informative comparisons with C. elegans.