Scott SP et al. (2000) European Worm Meeting "Starvation stress and trade-offs in C. elegans"

Lithgow GJ, Scott SP, Jenkins NL, McColl G, Walker DW

[European Worm Meeting, 2000]

Ageing has been postulated to result from late life detrimental effects of genes that act beneficially early in life. Evidence to support this hypothesis has been provided by the competitive fitness of a single-gene mutant in Caenorhabditis elegans that increases mean and maximum lifespan by up to 80%. The gene, age-1, encodes a phosphatidylinositol 3-kinase catalytic subunit that functions in an insulin-like signalling pathway. This pathway controls progression through normal development and determines adult stress resistance. Under standard laboratory conditions there are no apparent costs associated with the age-1(hx546) mutation. However, a trade-off between longevity and competitive fitness was observed under conditions of cyclical starvation that approximate the natural environment and hence have greater relevance to the evolutionary history of C. elegans. Further investigation indicates that the length of starvation period affects which life stages contribute to subsequent generations and, unexpectedly, it is young adults rather than dauers in which the trade-off occurs. Examination of dauers of both age-1 and wild type strains after starvation indicates that, in contrast to current belief, there are costs associated with this life stage.

Woodruff, Gavin et al. (2015) International Worm Meeting "Notable characteristics of Caenorhabditis sp. 34, a novel species associated with figs."

Kanzaki, Natsumi, Woodruff, Gavin, Kikuchi, Taisei

[International Worm Meeting, 2015]

In 2013, a novel nematode species was discovered in the fresh figs of Ficus septica in Okinawa. Subsequent DNA sequencing revealed that this species belongs to Caenorhabditis. Here, some biological characteristics of C. sp. 34 are described. C. sp. 34 is an exceptional member of Caenorhabditis in a number of respects. C. sp. 34 animals can grow to be nearly twice as long as C. elegans (1.5-2 mm), and take about twice as long to develop (~8 days at 20degC). This length difference in adults is largely due to post-embryonic events as C. sp. 34 embryos are about 19% longer than C. elegans embryos. C. sp. 34 sperm are enormous (about three times longer in diameter than C. elegans sperm), whereas the C. sp. 34 female tail spike is about half as long as that of the C. elegans hermaphrodite. However, examination of Hoechst-stained diakinesis oocytes reveals that, like C. elegans, C. sp. 34 has six chromosomes. No differences in the number of intestinal nuclei were observed between C. sp. 34 and C. elegans. Preliminary fluorescent microscopy observations suggest that the somatic nucleus number, hypodermal nucleus ploidy, and genome size of C. sp. 34 is comparable to that of other Caenorhabditis species. Additionally, mating tests show that C. sp. 34, C. sp. 35 (which is also fig-associated), and C. elegans are distinct biological species, and reproductive barriers include lack of sperm transfer, lack of fertilization, and embryonic inviability. This work has been concurrent with a larger collaborative effort, whose ongoing efforts include investigations into genomics, population genetics, and developmental biology. C. sp. 34 is an exciting species that will likely prove fruitful in future evolutionary studies.

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

Koutsovoulos, Georgios, Chandrasekar, Sinduja, Stevens, Lewis, 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].

Kimble JE et al. (2000) Midwest Worm Meeting "Genetics of prepattern formation in the C. elegans gonad"

Siegfried KR, Kimble JE

[Midwest Worm Meeting, 2000]

During organ development many tissue types must be specified and organized to form a functional organ. We are interested in how the different tissues that comprise an organ become organized. To address this problem, we have taken a genetic approach to identify genes that are required for patterning the somatic gonadal tissues in C. elegans. During early gonadogenesis, blast cells and regulatory cells are specified. Subsequently, somatic gonadal blast cells rearrange to set up the pattern of the adult organ. This "prepattern" of the adult tissues is called the somatic primordium (SP). In both hermaphrodites and males, SP formation is crucial for proper organization of the gonadal tissues. The SP differs between sexes reflecting the dimorphic organization of tissues seen in adult gonads. We have isolated a group of mutants in which SP formation is disrupted in a sex-specific manner. In hermaphrodites, the early somatic gonadal lineage is aberrant and the SP fails to form. This failure in SP formation results in a severely disorganized organ and sterility. In males, however, the early lineage is normal and SP formation is not affected. We postulate that, during early gonadogenesis, cells required for instructing hermaphrodite SP formation are not specified. We have identified seven genes with this mutant phenotype. These genes show dose sensitivity and appear to define a developmental pathway. We are in the process of characterizing these mutants genetically, phenotypically and molecularly to understand how the somatic gonadal tissues are patterned during organogenesis.

Sugimoto, Asako et al. (2017) International Worm Meeting "Establishing genetic techniques to study Caenorhabditis sp. 34, a sister species of C. elegans."

Kanzaki, Natsumi, Hoshi, Yuki, Kumagai, Ryohei, Sugimoto, Asako, Kikuchi, Taisei, Namai, Satoshi, Tsuyama, Kenji

[International Worm Meeting, 2017]

Caenorhabditis sp. 34 is a sister species of C. elegans recently isolated from the syconia of the fig Ficus septica on Ishigaki Island, Japan (see abstract by T. Kikuchi, et al.). C. sp. 34 is gonochoric and shares typological key characters with other Elegans supergroup species, but strikingly, adults are nearly twice as long as C. elegans. The optimal culture temperature for C. sp. 34 is significantly higher (27 deg C) than that of C. elegans (20 deg C). Young adult males and females tend to form clumps, and Dauer larvae are rarely observed in laboratory culture conditions. Recently the C. sp. 34 genome assembly was produced into six chromosomes (see abstract by T. Kikuchi, et al.). The marked differences from C. elegans in morphology, behaviors and ecology, and the availability of the complete genome sequence make C. sp. 34 highly attractive for comparative and evolutionary studies. To make C. sp. 34 genetically tractable, we have been developing genetic and molecular techniques and tools. Stable transgenic lines of C. sp.34 could be obtained by microinjecting marker plasmids commonly used in C. elegans, although the efficiency was lower than that in C. elegans. Both soaking and feeding RNAi was as effective as in C. elegans. A panel of antibodies against C. elegans proteins successfully recognized expected structures in C. sp. 34 by immunofluorescence. Thus, many of the rich genetic and molecular resources for C. elegans can be directly used for C. sp. 34 studies. We well present some of the comparative analyses of gene functions regarding the body size, germ cell formation and sex determination.

Kiontke, Karin C. et al. (2013) International Worm Meeting "The latest update on Caenorhabditis species, their ecology, phylogeny, and morphology."

Kiontke, Karin C., Fitch, David H. A., Felix, Marie-Anne

[International Worm Meeting, 2013]

Since we reported on Caenorhabditis biodiversity in 2011, 13 new species have been discovered. The number of species in culture is now 36, and 50 species are known. Most new species were isolated from rotting plant material, but two were found in fresh figs (N. Kanzaki pers. comm.) and one in the hind gut of a millipede (W. Sudhaus pers. comm.). Three of the new species were isolated from temperate regions, the others from tropical regions. Preliminary phylogenetic analyses with molecular data for 36 species confirm the existence of two well-supported large sister clades, the Elegans super-group with now 21 species and the Drosophilae super-group with 11 species. C. plicata, C. sp. 1 and C. sonorae as well as a C. sp. 21 branch off basally. Still, no sister species of C. elegans has been found. Hybridization is now observed in crosses of 5 species pairs (C. angaria - C. sp. 12, C. briggsae - C. sp. 9, C. remanei - C. sp. 23, C. sp. 5 - C. sp. 26, C. sp. 8 - C. sp. 24), providing opportunity for studying the evolution of hybrid incompatibility in Caenorhabditis. In at least one case, crosses between individuals from some but not all populations show reproductive isolation, suggesting incomplete speciation. Using light and scanning electron microscopy, we are evaluating morphological characters of all cultured species in detail. Across Caenorhabditis, the morphological diversity is large, especially in features of the male tail and the stoma. However, no or only subtle differences are found between many species of the Elegans super-group. Mapping phenotypic characters onto the phylogeny shows extensive homoplasy (convergent evolution or secondary loss) across all character complexes. Morphological, biogeographical, ecological, sequence, and taxonomic data on all Caenorhabditis species is now available through an open-access online database RhabditinaDB (http://wormtails.bio.nyu.edu/Databases). Strains of most species are available through the CGC.

Kiontke, Karin C. et al. (2009) International Worm Meeting "New Caenorhabditis species: phylogeny and evolution."

Fitch, David H. A., Felix, Marie-Anne, Kiontke, Karin C.

[International Worm Meeting, 2009]

Recently, nine new Caenorhabditis have been discovered, bringing the number of Caenorhabditis species in culture to nineteen, eleven 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 and 11) group within the so-called Elegans group of Caenorhabditis, with C. elegans being the first branch. Although none of them is the sister species of C. elegans, C. sp. 5 and C. sp. 9 are close relatives of C. briggsae. C. sp. 9 can hybridize with C. briggsae in the laboratory. Of the remaining new species, C. sp. 7 branches off between C. elegans and C. japonica. Three of these species, C. sp. 7, C. sp. 9 and C. sp. 11 have been chosen for genome sequencing. Four further new species branch off before C. japonica within a monophyletic clade which also comprises C. sp. 3 and C. drosophilae. 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 seven 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. Other characters, like the shape of the stoma and the male tail, introns, susceptibility to RNAi and genome size are being evaluated in the context of the phylogeny. 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 few years. There is no indication that we are even close to knowing all species in this genus.

Kikuchi, T. et al. (2017) International Worm Meeting "Evolutionary insights into the C. elegans biology from the morphology, ecology and genome of the sister species Caenorhabditis sp. 34."

Wang, J., Kanzaki, N., Kikuchi, T., Sugimoto, A., Tanaka, R., Berriman, M., Woodruff, G., Tsai, I., Sternberg, P.

[International Worm Meeting, 2017]

One of a few missing pieces of C. elegans to be an exemplary model organism is a 'sister' species which provide deep evolutionary interpretations of identified biological phenomena. C. briggsae is the most widely used satellite model, but at the level of DNA sequence, this species is as divergent from C. elegans as humans are from mice. Other species including C. brenneri and C. remanei have similarly long phylogenetic distances from C. elegans. The gonochoric nematode C. sp. 34, recently isolated from fresh syconia of the fig Ficus septica in Ishigaki Island, Japan, is the long-sought sister species of C. elegans. C. sp. 34 shares typological key characters with other Elegans supergroup species, however the body size is much larger as the adults have nearly twice body length of those of C. elegans. C. sp. 34 occurs mainly in fresh syconia and are vectored by fig wasps. The C. sp. 34 genome assembly was produced using multiple technologies and manually finished into six chromosomes. The 123 Mb assembly is now the second nematode species after the C. elegans for which sequence information comprise solely in chromosomes. By sequencing the males and females of C. sp. 34, we have shown C. sp. 34 possess a XO sexual system. A total of 21,609 gene models were predicted in the nuclear genome and orthologues clustering was inferred between C. sp. 34 and 9 other Caenorhabditis species, confirming its close relationship to C. elegans. Divergence time estimation placed the separation of the two species ~120 million generations ago. LTR retrotransposons are highly expanded in the C. sp. 34 genome, which may be one of driving forces of the drastic evolution of C. sp. 34. On the other hand, gene losses in 7TM GPCR families are clear in the genome, reflecting the characteristic lifecycle. Considering the significant differences in body size, developmental processes, behaviours and lifestyles between the two species, our study on C. sp. 34 provides an outstanding platform to perform comparative evolutionary biological studies.

Karin Kiontke et al. (2008) Development & Evolution Meeting "New Phylogeny Of Caenorhabditis Including Recently Discovered Species"

David Fitch, Karin Kiontke, Marie-Anne FELIX

[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.

Castaneda, P.G. et al. (2017) International Worm Meeting "Regulation of communication between the spermatheca and the sp-ut valve."

Cram, E.J., Castaneda, P.G.

[International Worm Meeting, 2017]

The Caenorhabditis elegans (C. elegans) spermatheca, the site for embryo fertilization, is a tube composed of a single layer of cells that undergo cyclic stretching, constriction, and relaxation as ~150 oocytes pass through the gonad and into the spermatheca. This feature makes the C. elegans spermatheca an ideal model in which to explore mechanotransduction machinery in smooth muscle-like cells. The spermatheca is made up of three regions: the distal constriction, the bag, and the spermatheca-uterine (sp-ut) valve. Immediately after oocyte entry, the sp-ut valve constricts. After ~10 minutes, the bag begins to constrict, and the valve relaxes allowing the fertilized embryo to exit the spermathca and enter the uterus. We have identified several components that regulate oocyte transit through the spermatheca, including the phospholipase plc-1, which is required for the spermatheca to constrict and push the fertilized egg through the sp-ut valve into the uterus. However, very little is known about how the sp-ut valve and the spermatheca bag coordinate the appropriate response for successful egg transits. To address this, we expressed GCaMP, a genetically-encoded calcium sensor, under a sp-ut valve specific promoter (tag-312), as well as a spermatheca specific promoter (fkh-6). By conducting a candidate RNAi screen, we have identified inx-12, plc-1, and fln-1 as required for proper coordination between the bag and the sp-ut valve. We are currently using quantitative calcium analysis and spermathecal bag and sp-ut valve specific RNAi strains to characterize these genes.