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[
International Worm Meeting,
2021]
Caenorhabditis brenneri is an outcrossing species of nematodes in the 'Elegans' supergroup (Rhabditida) formally described by Sudhaus and Kiontke in 2007. C. brenneri is one of the most genetically diverse eukaryotes, roughly every tenth nucleotide is polymorphic, which makes it comparable to hyperdiverse bacteria (Dey et al. 2013). To study such a tremendous amount of diversity on the genome-scale, we need high-quality data and a chromosome-scale reference genome. We created a super-inbred C. brenneri strain VX0223 (300 generations of inbreeding) to remove the residual heterozygosity and constructed a telomere-to-telomere genome assembly using highly accurate long-reads, short-reads, and genome-wide chromatin organization data, as well as full-length transcript sequencing and RNA-seq for the genome annotation. We have shown that C. brenneri has a similar pattern of genome organization to other Caenorhabditis species, with a higher gene density in the central regions of chromosomes and the peripheral parts of chromosomes enriched with repeats. However, the percentage of the repetitive elements in the genome is lower than in other outcrossing species of Caenorhabditis, only 16.3% (C. remanei and C. inopinata have 23% and 30%). That is inconsistent with the previously reported higher repeat abundance in C. brenneri (Feschotte et al. 2009, Fierst at al. 2015), which is probably connected to the higher duplication level and redundancy in the previously available genome assemblies (caePb2 and GCA_000143925.2).
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[
International Worm Meeting,
2009]
The molecular differences of the four Caenorhabditis species C. elegans, C. briggsae, C. remanei and C. brenneri are currently of great interest, however little is known about development. Zhao et al. (2008) reported an automatic lineage of C. briggsae and came - based mostly on the cleavage pattern and cell positions - to the conclusion that the embryogenesis of the two species is very similar. We now present detailed 4D analyses of the species including the terminal differentiation patterns. All analyses including bioinformatical quantifications of cell behaviour show a huge similarity between those species. Immunochemical analyses of the tissue distributions only reveal a difference in the intestinal differentiation of C. brenneri. Interestingly hybrid embryos always appear to fail in different ways in embryogenesis.
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[
International Worm Meeting,
2009]
The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing of the genomes of C. elegans and a second hermaphrodite, C. briggsae, was facilitated in part by the low amount of natural heterozygosity, which typifies selfing species. Ongoing genome projects for gonochoristic Caenorhabditis species seek to approximate this condition by intense inbreeding prior to sequencing. We found that despite this inbreeding, the heterozygous fraction of the whole genome shotgun assemblies of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, is considerable. We demonstrated experimentally that independently assembled sequence variants in C. remanei and C. brenneri are allelic. We developed gene-based approaches for recognizing heterozygous regions of WGS assemblies. We also developed a simple method for quantifying heterozygosity that can be applied to assemblies lacking gene annotations. Consistently we found that ~10% and 30% of the C. remanei and C. brenneri genomes, respectively, are represented by two alleles in the assemblies. Heterozygosity is restricted to autosomes and its retention is accompanied by substantial inbreeding depression, suggesting that it is caused by multiple recessive deleterious alleles and not merely by chance. Both the overall amount and chromosomal distribution of heterozygous DNA is highly variable between assemblies of close relatives produced by identical methodologies, and allele frequencies have continued to change after strains were sequenced. Our results highlight the impact of mating systems on genome sequencing projects and suggest that care must be exercised when analyzing sequences from shotgun assemblies.
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[
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].
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[
International C. elegans Meeting,
1995]
Two new gonochoristic Caenorhabditis ssp. were discovered in the rotting tissue of saguaro cacti in the Sonoran Desert near Tucson (Arizona). I present a cladogram of C. plicata, the two new species and a group of all other Caenorhabditis spp. (Eu-Caenorhabditis). Apomorphic characters of Caeno- rhabditis include: arrangement of bursal papilla as 2/4+3, 6th papilla enlarged at the base, and spicules with a dorsal velum. The two new species possess open bursae, which indicates a basal position in the cladogram. However, the first species branchis C. plicata which lacks a pharyngeal collar. All other Caenorhabditis spp. possess this collar as an apomorphic character. The second branch is Caenorhabditis sp.-1. An outward directed 5th (instead of 4th) papilla is the apomorphic character for the monophyletic group consisting of Caenorhabditis sp.-2 and its sister group Eu-Caenorhabditis. Eu-Caenorhabditis is united by apomorphic characters including: bursa anteriorly closed with serrate anterior margin, praecloacal hook, and pointed spicule tips. Apomorphic characters of Caenorhabditis sp.-1 are: spicules massive with two tips each, edge of bursa smooth. The nonwaving dauerlarvae are phoretic on the cactophylic fruit fly, Drosophila nigrospiracula. Caenorhabditis sp.-2 is a comparatively small oviparous species that carries a maximum of only 3 eggs in the uterus at a time. It lacks the three lateral lines that typify Caenorhabditis, and its spicules are highly complex.
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[
Evolutionary Biology of Caenorhabditis and Other Nematodes,
2010]
Since 2007, 13 new Caenorhabditis species have been discovered, bringing the total number of Caenorhabditis species in culture to 24. The majority of these new species were found through searches focusing on rotting fruits. To elucidate the relationships of the new species to the five species with sequenced genomes, we used sequence data from two rRNA genes and nine protein-coding genes. Several of these genes were identified as well-conserved, single-copy orthologs in the genomes of the five genome-sequenced species. With this dataset, we obtain almost complete resolution of the Caenorhabditis phylogeny. Our updated phylogeny confirms the existence of two major groups within Caenorhabditis. One group, contains all genome sequenced species and 10 further species. We call this group the Elegans group. The second group, the Drosophilae group, comprises C. drosophilae C. sp. 3 (PS1010) and 5 additional species. C. sp. 1 and C. plicata form the first two branches of the Caenorhabditis tree. C. elegans and C. briggsae have a cosmopolitan distribution. C. remanei and C. brenneri are also widely distributed, but C. remanei is found only in temperate zones whereas C. brenneri lives in tropical zones. Among the new species, some have been encountered several times, esp. C. sp. 11, found on La Runion in the Indian Ocean, the Cape de Verde Islands in the Atlantic, Guyana in S. America, and on Hawaii. Other species appear to have more limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States. Several species can co-occur in the same location or even in the same fruit. So far, it is not possible to infer a center of origin for the genus. Hermaphroditism evolved three times independently in Caenorhabditis, each time in a terminal lineage: C. elegans, C. briggsae, and C. sp. 11. The evolution of only two morphological features is fully congruent with the molecular phylogeny. A pointed spicule. evolved prior to the branch to C. elegans; a narrow fan and spiral copulation evolved in the stem species of C. sp. 3, 8 and 12. All other features show some degree of homoplasy, e.g. the serrated edge of the fan, the anteriorly closed fan, the position of the anterior dorsal ray and the hook.
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[
Development & Evolution Meeting,
2008]
The majority of nematodes are gonochoristic (dioecious) with distinct male and female sexes, but the best-studied model species, Caenorhabditis elegans, is a self-fertile hermaphrodite. The sequencing and assembly of the genomes of C. elegans and a second hermaphrodite, C. briggsae, was facilitated in part by the natural homozygosity which typifies highly selfing species. Ongoing genome projects for gonochoristic Caenorhabditis species seek to approximate this condition by intense inbreeding prior to sequencing. We used simple computational and experimental methods for recognizing heterozygous regions in whole-genome shotgun assemblies to show that despite this effort, large fractions of the genomes of three gonochoristic Caenorhabditis species, C. brenneri, C. remanei, and C. japonica, retained heterozygosity. This heterozygosity is restricted to autosomes and is accompanied by substantial inbreeding depression, suggesting that it is maintained by the presence of multiple recessive deleterious alleles. Because deleterious variation is universal for outbreeding species, our results highlight the importance of considering mating systems and population genetics in genome sequencing projects. Finally, our findings suggest that the rarity of hermaphroditic nematode species can be explained in part by the difficulty of overcoming inbreeding depression by incipient self-fertile hermaphrodites.
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[
Evolutionary Biology of Caenorhabditis and Other Nematodes,
2010]
Since 2007, 13 new Caenorhabditis species have been discovered, bringing the total number of Caenorhabditis species in culture to 24. The majority of these new species were found through searches focusing on rotting fruits. To elucidate the relationships of the new species to the five species with sequenced genomes, we used sequence data from two rRNA genes and nine protein-coding genes. Several of these genes were identified as well-conserved, single-copy orthologs in the genomes of the five genome-sequenced species. With this dataset, we obtain almost complete resolution of the Caenorhabditis phylogeny. Our updated phylogeny confirms the existence of two major groups within Caenorhabditis. One group, contains all genome sequenced species and 10 further species. We call this group the Elegans group. The second group, the Drosophilae group, comprises C. drosophilae C. sp. 3 (PS1010) and 5 additional species. C. sp. 1 and C. plicata form the first two branches of the Caenorhabditis tree. C. elegans and C. briggsae have a cosmopolitan distribution. C. remanei and C. brenneri are also widely distributed, but C. remanei is found only in temperate zones whereas C. brenneri lives in tropical zones. Among the new species, some have been encountered several times, esp. C. sp. 11, found on La Runion in the Indian Ocean, the Cape de Verde Islands in the Atlantic, Guyana in S. America, and on Hawaii. Other species appear to have more limited distributions, for example C. sp. 5 appears to be restricted to China, C. sp. 7 to West Africa and C. sp. 8 to the Eastern United States. Several species can co-occur in the same location or even in the same fruit. So far, it is not possible to infer a center of origin for the genus. Hermaphroditism evolved three times independently in Caenorhabditis, each time in a terminal lineage: C. elegans, C. briggsae, and C. sp. 11. The evolution of only two morphological features is fully congruent with the molecular phylogeny. A pointed spicule. evolved prior to the branch to C. elegans; a narrow fan and spiral copulation evolved in the stem species of C. sp. 3, 8 and 12. All other features show some degree of homoplasy, e.g. the serrated edge of the fan, the anteriorly closed fan, the position of the anterior dorsal ray and the hook.
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[
Development & Evolution Meeting,
2008]
Recently, seven new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to 17, 10 of which are undescribed. To elucidate the relationships of the new species to the five species with sequenced genomes, we have used sequence data from two rRNA genes and several protein-coding genes for reconstructing the phylogenetic tree of Caenorhabditis. Four new species (spp. 5, 9, 10, 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Whereas none of them is likely to be the sister species of C. elegans, we now know of two close relatives of C. briggsae-C. sp. 5 and C. sp. 9. C. sp. 9 can hybridize with C. briggsae in the laboratory [see abstract by Woodruff et al.]. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. This species is easier to cultivate than C. japonica and may be a better candidate for comparative experimental work. Two of the new species branch off before C. japonica as sister species of C. sp. 3 and C. drosophilae+C. sp. 2, respectively. Only one of the new species, C. sp. 11, is hermaphroditic. The position of C. sp. 11 in the phylogeny suggests that hermaphroditism evolved three times within the Elegans group. Two of the new species were isolated from rotting leaves and flowers, and five from rotting fruit. Rotting fruit is also the habitat in which C. elegans has been found to proliferate (Barriere and Felix, Genetics 2007) and from which C. briggsae, C. brenneri and C. remanei were repeatedly isolated. This suggests that the habitat of the stem species of Caenorhabditis after the divergence of the earliest branches (C. plicata, C. sonorae and C. sp. 1) was rotting fruit. The rate of discovery of new Caenorhabditis species has steadily increased since the description of C. elegans in 1899, with a leap in the last two years. There is no indication that we are even close to knowing all species in this genus.
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[
International Worm Meeting,
2017]
Biotic interactions are ubiquitous and require information from ecology, evolutionary biology, and functional genetics in order to be completely understood. However, study systems that are amenable to investigations in such disparate fields are rare. Figs and fig wasps are a classic system for ecology and evolutionary biology with poor functional genetics; C. elegans is a classic system for functional genetics with an historically poorly-described ecology. In order to help bridge these disciplines, here we describe the natural history of a close relative of C. elegans, C. sp. 34, that is associated with the fig Ficus septica and its pollinating Ceratosolen wasps. To understand the natural context of fig-associated Caenorhabditis, fresh F. septica figs from four Okinawan islands were sampled, dissected, and observed under microscopy. Caenorhabditis was found in all islands where F. septica figs were found. Caenorhabditis was routinely found in the fig interior and almost never observed on the outside surface. DNA sequencing of fig-derived animals revealed that they share nearly identical cytochrome oxidase I sequence with C. sp. 34. Caenorhabditis was only found in pollinated figs, and Caenorhabditis was more likely to be observed in figs with more foundress pollinating wasps. Actively reproducing Caenorhrabditis dominated younger figs, whereas older figs with emerging wasp progeny typically harbored Caenorhabditis dispersal (likely dauer) larvae. Additionally, Caenorhabditis was observed dismounting from plated Ceratosolen pollinating wasps. Caenorhabditis was never found on non-pollinating, parasitic Philotrypesis wasps. And, Caenorhabditis was only observed in F. septica figs among six Okinawan Ficus species sampled. These observations suggest a natural history where C. sp. 34 proliferates in young F. septica figs and disperses from old figs on Ceratosolen pollinating fig wasps. The fig and wasp host specificity of this Caenorhabditis is highly divergent from its close relatives and frames hypotheses for future investigations. This natural coincidence of the fig/fig wasp and Caenorhabditis study systems sets the stage for an integrated research program that can help to explain the evolution of interspecific interactions.