Townsend SR et al. (1994) Worm Breeder's Gazette "C. elegans Molecular Genetics and Long PCR."

Savage C, Padgett RW, Finelli AL, Xie T, Townsend SR

[Worm Breeder's Gazette, 1994]

C. elegans Molecular Genetics and Long PCR Scott R. Townsend, Cathy Savage, Alyce L. Finelli, Ting Xie, and Richard W. Padgett, Waksman Institute and Department of Molecular Biology and Biochemistry, Rutgers University, Piscataway, NJ 08855

Teterina, Anastasia et al. (2019) International Worm Meeting "Mode of reproduction drives the distribution of polymorphism across the genome: theory and empirical tests in Caenorhabditis nematode."

Phillips, Patrick, Jovelin, Richard, Teterina, Anastasia, Cutter, Asher, Willis, John

[International Worm Meeting, 2019]

Genomic polymorphism and recombination patterns tend to be positionally correlated because of linked selection. For selfing nematodes Caenorhabditis elegansand C. briggsae, recombination rate and natural genetic variation are high in chromosome "arms" and low in the central parts of chromosomes (Rockman et al. 2009; Andersen et al. 2012; Ross et al. 2011; Thomas et al. 2015). To explore how outcrossing might affect this distribution, we studied C. remanei, an obligate outcrossing species, which has a significantly larger effective population size than C. elegans and C. briggsae. We variation in polymorphism and recombination rates across the C. remanei genome using a newly constructed PacBio-HiC chromosome-level genomic assembly and a high-density genetic map. Comparing available whole-genome data for C. elegans and C. briggsaestrains with newly generated whole-genome sequences of several dozen C. remaneilines obtained from a single natural population from Ontario, Canada, we find that the landscape of recombination dominates the pattern of genomic variation in these Caenorhabditis species, regardless of differences in mating system and population size. While autosomes show similar patterns across species, the X chromosome in C. remanei has a different distribution of genomic polymorphism, which is similar to its autosomes, possibly due to higher effective population size and mode of reproduction. To address these empirical patterns more systematically, we performed individual-based forward genetic simulations in SLiM3, varying the fraction of outcrossing individuals in populations, the selection regime, and the chromosome-level landscape of recombination. These simulations show that while complete selfing leads to a uniform distribution of variation across the genome, even a small degree of outcrossing allows recombination and selection to generate the pattern observed across these nematode species. So different species have similar patterns of variation across their chromosomes even while their base levels of within-species polymorphism are very similar. This is caused by the interaction of selection, sex and recombination, which means that there must be more outcrossing in C. elegans populations than currently thought.

Martinelli SD et al. (1995) International C. elegans Meeting "ACEDB"

Durbin RM, Martinelli SD

[International C. elegans Meeting, 1995]

We hope to provide a demonstration of the current state of the ACeDB worm database on Unix workstations, and if possible Apple Macintosh, throughout the poster sessions. This will be based on the new version 4 release of the acedb software (Jean Thierry-Mieg, Richard Durbin and numerous others), which contains many new features for greater efficiency, more flexible printing, and display of new features.

(2024) Development "The people behind the papers - Thomas Mullan and Richard Poole."

[Development, 2024]

Asymmetric cell divisions can produce daughter cells of different sizes, but it is unclear whether unequal cell cleavage is important for cell fate decisions. A new paper in Development explores the role of unequal cleavages in Caenorhabditis elegans embryos. To learn more about the story behind the paper, we caught up with first author Thomas Mullan and corresponding author Richard Poole, Associate Professor of Developmental Biology at University College London, UK.

Ghosh, Rajarshi et al. (2013) International Worm Meeting "Evolution of avermectin resistance in C. briggsae."

Kruglyak, Leonid, Cutter, Asher, Jovelin, Richard, Ghosh, Rajarshi, Wang, Wei, Thomas, Cristel

[International Worm Meeting, 2013]

Several nematode species have evolved resistance to the widely used anthelmintic avermectins (AVM). AVM is produced naturally by S.avermitilis, a ubiquitous soil bacterium. As many nematodes spend part of their life cycle in contact with soil, they are likely to encounter S.avermitilis. Widespread AVM resistance may be a result of different nematode species' ability to counter a common selective pressure, namely the toxins produced by S. avermitilis. To test this hypothesis we surveyed AVM resistance in diverse nematode species. We found that resistance to AVM and to S. avermitilis was prevalent in this phylum. To identify the genetic basis of natural AVM resistance we focused on C. briggsae. We found that two divergent isolates of C. briggsae differed significantly in their responses to AVM. Using QTL mapping approach with these two strains , we identified a significant locus on Chromosome II underlying responses to AVM. We also surveyed 50 isolates of C. briggsae for responses to AVM and found that they exhibit wide variation. The pattern of variation in responses to AVM correlated significantly with the observed phylogeographic pattern in C. briggsae, with temperate isolates being more likely to be resistant than tropical ones. To gain insights into the evolution AVM resistance in C. briggsae, we obtained whole genome sequences of these isolates. Using this data we confirmed that glc-1, the causative gene for natural AVM resistance in C. elegans, is the result of a duplication of another GluCl subunit in the elegans lineage. Thus glc-1 is absent in C. briggsae suggesting that the genetic mechanisms of natural resistance to AVM in C. briggsae are likely different from C. elegans. The sequence data will help us determine if variation in candidate targets for AVM correlate with the pattern of resistance in C. briggsae and map the genetic basis of differences in responses to AVM in C. briggsae .

Herman RK et al. (1997) Worm Breeder's Gazette "STATUS OF THE CAENORHABDITIS GENETICS CENTER (CGC)"

Herman RK, Stiernagle TL

[Worm Breeder's Gazette, 1997]

May 31, 1997 will mark the end of our current five-year contract with the NIH National Center for Research Resources, which supports the activities of the CGC. The activities in St. Paul have involved primarily the acquisition, maintenance and distribution of stocks and information about stocks, acquisition and maintenance of the C. elegans bibliography, and publication and distribution of The Worm Breeder's Gazette (WBG) and WBG Subscriber Directory. Genetic nomenclature and the genetic map have been managed for the period 1992-1997 by Jonathan Hodgkin (CGC Map Curator) on a subcontract. Currently, the subcontract provides half of Sylvia Martinelli's salary, plus travel and minor expenses. Additional support from within the MRC Laboratory of Molecular Biology and the Sanger Centre has been used to fund other essential resources such as computer equipment, as well as Jonathan's and Richard Durbin's time. Richard has been involved in mapkeeping through his work on ACeDB. We are pleased that Jonathan, Richard and Sylvia agreed to continue their work for another five years. We have submitted an application for a new five year contract that would include a subcontract for nomenclature and mapkeeping on essentially the same terms as before. A description of the nomenclature and mapkeeping activities is given in the following abstract. We are grateful to Leon Avery for setting up our CGC gopher server and also for arranging for the electronic submission of WBG abstracts (as well as abstracts for various C. elegans meetings). His C. elegans WWW server has become an essential resource for the worm community. We were therefore pleased to include Leon (only 5% effort) in a second subcontract as part of our new CGC application. We welcome comments and suggestions about any of the CGC activities.

Gimond, Clotilde et al. (2013) International Worm Meeting "Strong outbreeding depression and low genetic diversity in the selfing Caenorhabditis sp. 11."

Gimond, Clotilde, Jovelin, Richard, Han, Shery, Ferrari, Celine, Cutter, Asher D., Braendle, Christian

[International Worm Meeting, 2013]

Theory and empirical study produce clear links between the evolution of mating systems and the fitness effects of breeding between close relatives in terms of inbreeding depression. The connections between mating systems and outbreeding depression, whereby fitness is reduced in crosses of unrelated individuals, however, are less well defined. Gonochoristic Caenorhabditis species are generally characterized by high population genetic variation whereas the selfing Caenorhabditis species, C. elegans and C. briggsae, show clear signs of outbreeding depression. Our aim was to further investigate the extent of inbreeding and outbreeding depression in the context of selfing, focusing on the third androdioecious species of Caenorhabditis, the undescribed, pan-tropical C. sp. 11. Analysis of nucleotide diversity in a collection of approximately 50 C. sp. 11 wild isolates revealed very little polymorphism compared to other Caenorhabditis species, indicating similar or lower levels of genetic diversity than the other two selfing species. Moreover, crosses between geographically separated C. sp. 11 isolates uncovered very strong outbreeding depression in F1 hybrid reproductive performance (offspring number, embryonic mortality). Outbreeding depression was significantly higher in F1 hybrids derived from inter-locality crosses compared to intra-locality crosses and highly variable depending on the parental strain combination, ranging from a 10 to > 50% decrease in larval offspring production relative to F1 pure strains. We also show that male mating efficiency is generally lower in C. sp. 11 strains than in the reference strains for C. elegans (N2) and C. briggsae (AF16). Thus, outbreeding depression appears to be a common feature of selfing Caenorhabditis species, and most pronounced in C. sp. 11. We propose that self-fertilization is a key driver of outbreeding depression, but that outbreeding depression need not evolve as a direct result of local adaptation per se.

Kelley S (2000) Brief Bioinform "Getting started with Acedb."

Kelley S

[Brief Bioinform, 2000]

Acedb is one of the more venerable pieces of Genomics software. Acedb was originally created in 1992 by Richard Durbin and Jean Thierry-Mieg to manage the data from the Caenorhabditis elegans mapping project and subsequently the C. elegans sequencing project. From beginnings as a C. elegans-specific tool, it has been continuously developed into a flexible suite of data management, display and scripting tools providing facilities for managing and annotation mapping information and DNA and peptide sequences.This paper gives a basic overview of the Acedb suite, and step-by-step guidance on how to download and install Acedb. It is intended to take an Acedb novice to stage where they can begin to experiment and explore the facilities that are available.

Sommer RJ (2008) Bioessays "Homology and the hierarchy of biological systems."

Sommer RJ

[Bioessays, 2008]

Homology is the similarity between organisms due to common ancestry. Introduced by Richard Owen in 1843 in a paper entitled "Lectures on comparative anatomy and physiology of the invertebrate animals", the concept of homology predates Darwin's "Origin of Species" and has been very influential throughout the history of evolutionary biology. Although homology is the central concept of all comparative biology and provides a logical basis for it, the definition of the term and the criteria of its application remain controversial. Here, I will discuss homology in the context of the hierarchy of biological organization. I will provide insights gained from an exemplary case study in evolutionary developmental biology that indicates the uncoupling of homology at different levels of biological organization. I argue that continuity and hierarchy are separate but equally important issues of homology.

Thomas, Cristel G. et al. (2013) International Worm Meeting "Population genomic variation in the outcrossing species Caenorhabditis remanei."

Cutter, Asher D., Willis, John H., Thomas, Cristel G., Jovelin, Richard, Wang, Wei, Fierst, Janna L., Phillips, Patrick C.

[International Worm Meeting, 2013]

Natural populations of C. elegans contain orders of magnitude fewer nucleotide polymorphisms and longer haplotype linkage blocks than their outcrossing Caenorhabditis relatives. These factors, together with the lack of a close outgroup to C. elegans, limit our ability to interpret patterns of within-species variation in C. elegans. To better understand how evolutionary forces interact to shape nematode genome evolution, we are investigating population polymorphism and divergence for C. remanei and its close relative C. sp. 23 by sequencing whole genomes of many wild isolates of these species. We combine two complementary approaches to investigate patterns of diversity in the genome of C. remanei. We used next-generation sequencing to gather whole-genome data from dozens of C. remanei isofemale inbred strains from multiple populations from Europe and North American and for several C. sp. 23 isofemale inbred strains from a single population in China. These strains are maintained in culture and are available to the worm community. We also directly sequenced genomes from single C. remanei individuals immediately collected from the field to minimize the effect of lab breeding. Consistent with previous results based on tens of genes, we find high nucleotide diversity for SNPs, indels and microsatellites in both C. remanei and C. sp. 23. This data provides a framework to quantify demographic and selective forces shaping nucleotide polymorphism across the entire genome and for testing hypotheses about the molecular evolution of focal gene classes. Our ongoing work is using this resource to understand the microevolution of small RNA genes, their downstream targets, and their upstream regulators. In addition, because these two species are partially interfertile, the collection of variants we uncovered makes this species pair an extraordinary system for addressing diverse questions in ecological and speciation genetics.