Antoine Barriere et al. (2005) International Worm Meeting "C. elegans out there: a high local genetic diversity and a low outcrossing rate"

Marie-anne Flix, Antoine Barriere

[International Worm Meeting, 2005]

Despite 40 years of studies in the laboratory, our knowledge of Caenorhabditis elegans biology in the wild is scarce. We describe the first systematic isolation of C. elegans individuals from natural populations. We present data on the ecology and genetics of these populations.We sampled in mainland France. Caenorhabditis elegans was found sometimes in soil, but mainly in rich, human-associated habitats: compost heaps, decaying leaf litter, sometimes associated with various invertebrates (snails, isopods). It was predominantly found in the dauer stage. On several occasions, we found it co-occurring with C. briggsae.We measured molecular diversity on four populations from France using Amplified Fragment Length Polymorphism (AFLP), a whole-genome fingerprinting technique. Molecular diversity of the species as a whole is low (=8.1 x 10-4 per nucleotide), comparable to that of humans, while relative molecular diversity found within a population is high and represent a significant proportion of worldwide diversity. We found a strong population structure, even between geographically close populations. However most alleles are shared between different populations, showing that migration is a major contributor to within-population diversity.An important question in C. elegans biology is the rate of outcrossing and the frequency of males in nature. Systematic sampling of worms as they crawled out of the soil revealed only 2 males out of 1135 individuals. We found that linkage disequilibrium is strong both within and between populations ; since even low outcrossing rates would break down linkage disequilibrium, this suggests that outcrossing is rare or even exceptional. Nonetheless, over four populations, we found several evidences of inter and intrachromosomal recombination between AFLP loci. A direct measure of heterozygote frequency with microsatellites in another set of wild populations revealed that the outcrossing rate is approximately 1%. Thus, both males and outcrossing do occur in nature, but at a low rate.

Verster, Adrian et al. (2009) International Worm Meeting "Examining Changes in Gene Function in Caenorhabditis nematodes using RNAi libraries."

Ramani, Arun, Felix, Marie-Anne, Mckay, Sheldon, Verster, Adrian

[International Worm Meeting, 2009]

Gene functions change throughout evolutionary history and understanding how this occurs is a key goal of molecular evolutionary biology. To date researchers have systematically looked at changes in gene function by comparing loss of function phenotypes in orthologs from different model organisms, such as S. cerevisiae and C. elegans. However, since there has been such a large evolutionary divergence between these organisms their body plans are so different and many phenotypes are impossible to compare. It is much more practical to compare phenotypes from organisms with similar body plans and ecological niches. Here we use Caenorhabditis nematodes to systematically look at changes in gene function through evolution because loss of function phenotypes map easily between species. In order to address this problem we are building an RNAi library for C. briggsae to look for changes in gene phenotype from those that were observed in C. elegans. Genome scale RNAi has been successfully used in C. elegans and thus we are going to use it in C. briggsae. In order to do this we take advantage of the sid-2 transgenic C. briggsae line (gratefully contributed by Marie-Anne Felix''s group) which has been shown to uptake RNAi by feeding. We will present preliminary screening data from the C. briggsae RNAi library and showcase the changes in gene function we have found so far.

Conroy, Brian et al. (2013) International Worm Meeting "The neuronal basis of food choice behavior in Caenorhabditis elegans."

Conroy, Brian, Haynes, Lillian, Morabe, Maria, Glater, Elizabeth, Macfarlane, Rachel, Chambers, Melissa

[International Worm Meeting, 2013]

Caenorhabditis elegans uses chemosensation to distinguish among various species of bacteria, their major food source (Ha et al., 2010; Shtonda and Avery, 2006). Although the neurons required for the detection of specific food-odors have been well-defined (Bargmann, 2006), less is known about the sensory circuits underlying the discrimination among the mixtures of odors released by bacteria. We plan to examine the neural machinery underlying bacterial preference among a diverse set of bacterial species. Does bacterial choice use one common neuronal mechanism or a diversity of mechanisms depending on the bacteria? Do some bacterial choices involve a single sensory neuron and others involve multiple sensory neurons? To address these questions, we are testing the food preferences of C. elegans for bacteria found in their natural habitats (kindly provided by Marie-Anne Felix, Institut Jacques Monod, Paris, France). We have found that C. elegans strongly prefers the odors of Providencia sp., Alcaligenes sp., and Flavobacteria sp., to Escherichia coli HB101, a commonly used food source for C. elegans. We have identified that the olfactory neuron AWC is necessary for this preference. We intend to test whether other amphid sensory neurons are also necessary for bacterial preference. In the future we will extend our analysis to other bacterial species to determine the diversity of the underlying neuronal mechanisms. Bargmann, C.I. (2006). http://www.wormbook.org. Ha, H.I., Hendricks, M., Shen, Y., Gabel, C.V., Fang-Yen, C., Qin, Y., Colon-Ramos, D., Shen, K., Samuel, A.D., and Zhang, Y. (2010). Neuron 68, 1173-1186. Shtonda, B.B., and Avery, L. (2006). J Exp Biol 209, 89-102.

Jonathan Hodgkin et al. (2008) C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting "Bacterial pathogens, inflammation and disease resistance mechanisms in C. elegans"

Jonathan Hodgkin, Freddie Partridge, Delia O'Rourke, Maria Gravato-Nobre, Dave Stroud

[C.elegans Aging, Stress, Pathogenesis, and Heterochrony Meeting, 2008]

An increasing number of bacterial species with pathogenic effects on C. elegans have been identified and studied, either by testing known pathogens from other systems, or by the discovery of nematode-specific diseases. These investigations shed light on basic and potentially conserved aspects of innate immunity: bacterial infection, host detection, response to infection and mechanisms of antibacterial defense. We have focused mainly on the coryneform pathogen Microbacterium nematophilum, which attacks the worm by rectal infection and causes a conspicuous tail swelling, akin to an inflammatory response. Genetic analysis of the infection has identified multiple host genes involved in infection, many of which affect properties of the rectal epithelia and the hypodermis. Some of these also affect infection and pathogenesis by other bacteria. A specialized rectal version of the ERK MAP kinase cascade is required for the swelling effect and for amelioration of infection, which is potentially lethal. The rectal inflammation response can also be elicited by other Gram-positive bacteria, such as some strains of Staphylococcus and a new species of Leucobacter; the latter was isolated from a naturally infected Japanese population of C. elegans (collected by Marie-Anne Felix). These different infections exhibit both common and pathogen-specific features. Microarray analysis has revealed the induction of a variety of genes after infection by M. nematophilum, notably those belonging to lysozyme and C-type lectin gene families. Expression analysis indicates that many are expressed in the alimentary tract (pharynx, gut or rectum), and some in complex gene-specific patterns within these tissues. RNAi knockdown and/or gene deletion knockouts demonstrate that several of these genes contribute significantly to antibacterial defence.

Blaxter, Mark et al. (2015) International Worm Meeting "The Caenorhabditis Genomes Project."

Stevens, Lewis, Chandrasekar, Sinduja, Koutsovoulos, Georgios, Blaxter, Mark

[International Worm Meeting, 2015]

The sequencing of the genome of Caenorhabditis elegans remains one of the milestones of modern biology, and this genome sequence is the essential backdrop to a vast body of work on this key model organism. "Nothing in biology makes sense except in the light of evolution" (Dobzhansky) and thus it is clear that complete understanding of C. elegans will only be achieved when it is placed in an evolutionary context. While several additional Caenorhabditis genomes have been published or made available, a recent surge in the number of available species in culture makes the determination of the genomes of all the species in the genus a timely and rewarding project.We have initiated the Caenorhabditis Genomes Project. From material supplied by collaborators we have so far generated raw Illumina short-insert data for sixteen species. Where possible we have also generated mixed stage stranded RNASeq data for annotation. The data are being made publicly available as early as possible (warts-and-all) through a dedicated genome website at htttp://caenorhabditis.bio.ed.ac.uk, and completed genomes and annotations will be deposited in WormBase as mature assemblies emerge. We welcome additional collaborators to the CGP, whether to assemble new genomes or to delve into the evolutionary history of favourite gene sets and systems.Species sequenced thus far in Edinburgh: Caenorhabditis afra, Caenorhabditis castelli, Caenorhabditis doughertyi, Caenorhabditis guadeloupensis, Caenorhabditis macrosperma, Caenorhabditis nouraguensis, Caenorhabditis plicata, Caenorhabditis virilis, Caenorhabditis wallacei, Caenorhabditis sp. 1, Caenorhabditis sp. 5, Caenorhabditis sp. 21, Caenorhabditis sp. 26, Caenorhabditis sp. 31, Caenorhabditis sp. 32, Caenorhabditis sp. 38, Caenorhabditis sp. 39, Caenorhabditis sp. 40, Caenorhabditis sp. 43.[Samples have been supplied by Aurelien Richaud, Marie-Anne Felix, Christian Braendle, Michael Alion, Piero Lamelza].

Chung, Kevin et al. (2015) International Worm Meeting "The neuronal basis of bacterial food odor preference."

Chambers, Melissa, Kan, Emily, Ota, Ryan, Chung, Kevin, Haynes, Lillian, Glater, Elizabeth

[International Worm Meeting, 2015]

Caenorhabditis elegans uses chemosensation to distinguish among various species of bacteria, their major food source 1-3. Although the neurons required for the detection of specific food-odors have been well-defined, less is known about the sensory circuits underlying the discrimination among the mixtures of odors released by different kinds of bacteria. We are examining the neural machinery underlying bacterial preference among a diverse set of bacterial species. Specifically, we are testing the food preferences of C. elegans for bacteria found in their natural habitats (kindly provided by Marie-Anne Felix, Institute of Biology of Ecole Normale Superieure, Paris, France). We have found that C. elegans prefers the odors of most species tested over E. coli. We have identified that the olfactory neuron AWC is involved in many preferences. We also find that some bacterial choices involve multiple sensory neurons with opposing roles. For example, in one choice in which wild-type animals prefer Providencia sp. (JUb39) over E. coli, the AWC neuron appears to be involved in increased preference for Providencia and the AWA neuron in increased preference for E. coli. In the future we will extend our analysis to additional bacterial species to determine the diversity of the underlying neuronal mechanisms.1. Harris, G. et al. Dissecting the Signaling Mechanisms Underlying Recognition and Preference of Food Odors. J. Neurosci. 34, 9389-9403 (2014).2. Ha, H. et al. Functional Organization of a Neural Network for Aversive Olfactory Learning in Caenorhabditis elegans. Neuron 68, 1173-1186 (2010).3. Shtonda, B. B. & Avery, L. Dietary choice behavior in Caenorhabditis elegans. J. Exp. Biol. 209, 89-102 (2006).

Gimond, Clotilde et al. (2011) International Worm Meeting "Phenotypic characterization of the tropical hermaphroditic species Caenorhabditis sp. 11."

Mauri, Alessandra, Ferrari, Celine, Gimond, Clotilde, Vigne, Paul, Callemeyn-Torre, Nicolas, Grimbert, Stephanie, Braendle, Christian, Poullet, Nausicaa

[International Worm Meeting, 2011]

The majority of Caenorhabditis species exhibits a male-female mode of reproduction, and hermaphroditism has evolved only twice, in C. elegans and C. briggsae. Recently, a third hermaphroditic species, C. sp. 11, has been identified by Marie-Anne Felix (strain JU1373, La Ruunion). Since then, the isolation of more than 30 additional C. sp. 11 wild isolates from La Reunion, Cap Verde, Puerto Rico, Hawaii, Guadeloupe and mainland South America (French Guiana, Brazil) indicates that this species occurs primarily, if not exclusively, in tropical regions. Here we present the results of our current phenotypic characterization of recently collected wild isolates of C. sp. 11 with the aims (i) to quantify the degree of intraspecific variation and its correlation with geographic origin, (ii) to test for plasticity and genotype-by-environment interactions in reproductive traits at different temperatures and (iii) to ask how C. sp. 11 phenotypic characteristics differ from the ones observed in C. elegans and C. briggsae. This survey focuses mainly on germline and reproductive features (e. g. germ cell number, sperm number and size, offspring number) and basic life history traits (e.g. male production, propensity to enter dauer, longevity). Our initial observations confirm that C. sp. 11 isolates are overall much more heat-tolerant (and less cold-resistant) than C. elegans isolates, e.g. they maintain their reproductive output at 27 deg C similar to tropical C. briggsae strains. Interestingly, there is also substantial variation in reproductive output among different C. sp. 11 isolates, and many isolates have a much reduced offspring number relative to N2 and AF16. This reduction in offspring number correlates with a much reduced sperm and germ cell number, and we are currently testing to what extent germline size and reproductive output are modulated by temperature.

Dubois, C. et al. (2017) International Worm Meeting "Efficient identification of candidate gene mutations by mapping-by-sequencing in the non-model nematode Oscheius tipulae."

Blaxter, M., Vargas-Velazquez, A., Besnard, F., Dubois, C., Felix, M-A., Koutsovoulos, G.

[International Worm Meeting, 2017]

Oscheius tipulae is a common free-living nematode in the same clade as the parasitic taxa Heterorhabditis and strongylids, and closer to the model species Caenorhabditis elegans than the outgroup Pristionchus pacificus. This hermaphroditic species is thus informative for comparative genetics, developmental and evolutionary studies. However, the genetic toolbox for non-model organisms such as O. tipulae is still underdeveloped. In model species with fully assembled and annotated genomes, mapping-by-sequencing has become a standard method to map and identify phenotype-causing mutations. Candidate variants are pinpointed using a cross to a divergent mapping strain and sequencing of a pool of mutant segregants (e.g. ref. 1). Chemical mutagenesis (EMS) performed about 15-20 years ago by Marie-Anne Felix's lab on the O. tipulae strain CEW1 generated several vulval development and other morphological mutants, including dumpy, roller and uncoordinated phenotypes (refs 2-6). Using the mapping-by-sequencing approach, a draft genome sequence for O. tipulae CEW1 and crosses with the divergent wild isolate JU170, we have identified for the first time relevant candidate genes for these phenotypes in O. tipulae. Our success suggests that a draft assembly with multiple scaffolds per chromosome is sufficient to perform mapping-by-sequencing. Other recent genetics tools such as CRISPR/Cas9 system have been developed and widely used on Caenorhabditis species to perform targeted mutagenesis, and we propose to confirm candidate genes by developing CRISPR/Cas9 system on O. tipulae. We argue here that the mapping-by-sequencing approach and genomic analysis tools can be easily used in non-model organisms. This brings non-model species firmly into genomics-enabled science, and provides tools to investigate the biology of non-model species and improve our understanding of evolution and developmental mechanisms. (1) Doitsidou et al. PLOS One 2011; (2) Felix et al. Nematology, 2000; (3) Dichtel et al. Genetics 2001; (4) Louvet-Vallee et al. Genetics 2003; (5) Dichtel-Danjoy et al. Dev Biol 2004; (6) Felix, Oscheius tipulae, WormBook, 2006.

Worthy, S. et al. (2017) International Worm Meeting "The neuronal and chemical basis of bacterial food odor preference."

Worthy, S., Rojas, G., King, J., Taylor, C., Doan, N., Phan, J., Glater, E.

[International Worm Meeting, 2017]

Food choice is critical for survival because organisms must choose food that is edible and nutritious and avoid pathogenic food. Odors are some of the most important cues that animals use to find and distinguish among foods. The nematode Caenorhabditis elegans uses chemosensation to distinguish among various species of bacteria, their major food source1-4. Although the neurons required for the detection of specific food-odors have been well-defined, less is known about the sensory circuits underlying the discrimination among the mixtures of odors released by different kinds of bacteria. We are examining the sensory neurons underlying bacterial preference among a diverse set of bacterial species. Specifically, we are testing the food preferences of C. elegans for bacteria found in their natural habitats (kindly provided by Marie-Anne Felix, Institute of Biology of Ecole Normale Superieure, Paris, France). We have found that C. elegans prefers the odors of most species tested over E. coli. We have identified that the olfactory neuron AWC is involved in many preferences. In addition, we have preliminary data identifying the attractive odorants released by these bacteria using solid-phase microextraction-gas chromatography/mass spectrometry (SPME-GC/MS). While it has long been known that C. elegans recognizes volatiles known to be released by bacteria in general, little is known about what specific volatiles C. elegans uses to discriminate among different species of bacteria. 1. Harris, G. et al. Dissecting the Signaling Mechanisms Underlying Recognition and Preference of Food Odors. J. Neurosci. 34, 9389-9403 (2014). 2. Zhang, C. et al. The Signaling Pathway of Caenorhabditis elegans Mediates Chemotaxis Response to the Attractant 2-Heptanone in a Trojan Horse-like Pathogenesis. J. Biol. Chem. 291, 23618-23627 (2016). 3. Ha, H. et al. Functional Organization of a Neural Network for Aversive Olfactory Learning in Caenorhabditis elegans. Neuron 68, 1173-1186 (2010). 4. Shtonda, B. B. & Avery, L. Dietary choice behavior in Caenorhabditis elegans. J. Exp. Biol. 209, 89-102 (2006).

Irina Kolotuev et al. (2005) International Worm Meeting "RHABDITIDA OF THE WORLD UNITE !!! EVOLUTION OF ORGANOGENESIS AND RING FORMATION IN THE VULVA"

Benjamin Podbilewicz, Irina Kolotuev

[International Worm Meeting, 2005]

The diversity of the Nematode species is enormous although the overall body plan of worms is conserved in evolution. We are interested in how such diversity was originated and whether we can identify specific changes in cell biological events (e.g. cell migration, cell division and cell fusion) responsible for morphological variability among Rhabditida species. Organogenesis of the vulva in the nematodes Caenorhabditis elegans and Pristionchus pacificus was described in detail (1,2). To study the evolution of vulva formation in related Rhabditida nematode species we participate in an international consortium studying differences in the molecular, lineage and cellular aspects of organogenesis (3). Ring shaped structures form the vulva in all studied species. We have found that different aspects of vulva formation such as cell migration, intratoroidal fusion sequence and final ring structure are diverse through the different species of the Rhabditida family. We also found a correlation between the vulval cell division orientation and the final number of vulval rings. While there is little variation in the number and structures of rings derived from the 1ry sublineage, the rings derived from the 2ry sublineage generate dramatic structural diversity. When primordial cells divide in the anterior-posterior axis, they give rise to two vulval rings. When the same cells divide in the left-right axis, they form one ring. The most external primordial cells form a single ring, independent of the axis of their division. We are creating a matrix of the data that will integrate with multidisciplinary findings from the other research groups of our consortium (Marie-Anne Felix, Ralf Sommer and David Fitch; see abstract by Kiontke et al.). In our search for evolution in the lab we have checked lin-11 mutant causing a cell transformation in the 2ry lineage. In lin-11 mutants, the cells that normally express the LLTN lineage pattern, transform to either LLLN or LLLL patterns. We predicted that according to our hypothesis, the L division might give 2 rings instead of 1 ring resulting from a T division. Indeed, we found lin-11 hermaphrodites with 8 rings instead of 7 in N2. (1) Development, 1999, 126, 691-699. (2) Dev Biol, 2004, 266, 322-333. (3) Supported by HFSP.