Tanaka, R. et al. (2013) International Worm Meeting "Quiescence of entomo-phoretic nematode Caenorhabditis japonica."

Kanzaki, N., Tanaka, R., Hirooka, Y., Kikuchi, T.

[International Worm Meeting, 2013]

Entomo-phoretic nematodes are not parasitic to insects but use insects for their transportation. Caenorhabditis japonica, a bacteria-feeding nematode, has a species-specific phoresy with a shield bug, Parastrachia japonensis, and its lifecycle is synchronized to the bug's life. The active dauer larvae (DL) show intensive host-seeking, high sensitivity to oxidative stress and less than 15 days of longevity without attaching the bug. On the other hand, quiescent DL on the bug survive more than 11 months. Thus, the quiescence associated with the bug seems an essential factor for nematode survivability. In the present study, survivabilities of quiescent and active DL were compared under several different conditions to examine the involvement of the bugs in nematode's longevity. Then transcripts and proteins were analyzed to compare gene expression between quiescent and active DL. The quiescent DL on the bug and active DL were kept in a container with 85% (dehydrated condition) or 97% (lightly dehydrated condition which immobilize the DL) of relative humidity (RH). The most active DL died in one week because of desiccation (85% RH) or fungal infection (97% RH). On the other hands, quiescent DL on the bug showed significantly higher survival rate under the same conditions. Further, the survivability of surface-sterilized active DL kept in 97% RH was almost the same as quiescent DL. Therefore, the bugs are likely to work as the shelter from dehydration, and are also providing anti-microbe activity to DL. The expressed genes and proteins also differed between quiescent and active DL. Expression of genes and proteins involved in several stress resistance, metabolic regulation and cuticle formation were significantly higher in quiescent DL. On the other hand, expression of genes and proteins involved in several metabolic related (activity regulation) were significantly higher in active DL. Our results suggest C. japonica DL use their host bug not only for transportation, but also as shelter from environmental stresses and microbe infection. Further, the quiescent stage-specific gene expression allows the extraordinary longevity of this stage.

John Spieth (2005) International Worm Meeting "An Update on the Caenorhabditis remanei, japonica and PB2801 Genome Sequencing Projects"

John Spieth

[International Worm Meeting, 2005]

In January 2004, NHGRI announced support for draft sequencing of three additional Caenorhabditis genomes; C. remanei, C. japonica and PB2801. The genome sequences, which are being generated at the Washington University (St. Louis) Genome Sequencing Center, and the accompanying analyses are meant to enhance the utility of the existing C. elegans finished, genome sequence. The sequencing plan calls for an approximate nine-fold coverage of each genome through a combination of whole-genome shotgun sequencing of short insert plasmids and fosmid ends, and two rounds of automated, primer-directed, sequence improvement. For each genome 12 randomly-chosen fosmid clones will be finished to help assess assembly accuracy, and approximately 10,000 ESTs will be generated to assist in, and assess the quality of, automated gene prediction. We will present an update on the sequencing, assembly and analysis of the three genomes.

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].

Kiontke K (1995) International C. elegans Meeting "MORPHOLOGY AND PHYLOGENETIC RELATIONSHIPS OF TWO NEW CAENORHABDITIS SPECIES FROM SAGUARO CACTUS ROT"

Kiontke K

[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.

Kiontke, Karin et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "Caenorhabditis phylogeny and character evolution"

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

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Since we last reported on Caenorhabditis diversity in 2011, 15 new species were found. Clearly, the rate of new species discovery has not reached a plateau. There are now 41 species in culture. 13 additional species are known from the literature only. Sampling efforts over decades could re-isolate only two previously described species, which also suggests that Caenorhabditis biodiversity is large. Most new species were found in rotting plant material, confirming the notion that Caenorhabditis are fruit-, flower-, and plant stem- nematodes. However, lately, several new species were first isolated from a phoretic host, putting an emphasis on the role of phoresy in the life cycle of most or all Caenorhabditis species. It also highlights the necessity for a better understanding of Caenorhabditis ecology. A new molecular phylogeny for 40 Caenorhabditis species, based on analyses with three different algorithms, confirms previously reconstructed relationships within the genus. Caenorhabditis contains three large monophyletic groups: the Elegans group, the Japonica group and the Drosophilae super group. Only 4 species are not part of these clades and branch off early. The three analyses yielded conflicting or weakly supported positions for 5 species. To solve some of these conflicts, we are adding data from more genes to our dataset. Light and scanning electron microscopic evaluation of morphology show that the diversity in phenotypic characters is large across the genus as a whole. However, most of this diversity is found in the Drosophilae super group and the basally branching species. Phenotypic diversity within the Elegans group is small in comparison. This is in contrast to the rate of molecular diversity, which is more uniform across all Caenorhabditis species. The analysis of phenotypic characters confirms that homoplasy is extensive and affects almost all characters studied. We continue to deposit morphological, biogeographical, ecological, sequence, and taxonomic data on all Caenorhabditis species in our open-access online database RhabditinaDB (http://wormtails.bio.nyu.edu/Databases). Information about Caenorhabditis isolates and ongoing and planned genome projects is also found in a WIKI on WormBase (http://evolution.wormbase.org/index.php/Main_Page).

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

David Fitch, Marie-Anne FELIX, Karin Kiontke

[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.

Woodruff, G. C. et al. (2017) International Worm Meeting "The natural history of a fig-associated Caenorhabditis."

Woodruff, G. C., Kanzaki, N., Phillips, P. C.

[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.

Sun, Simo et al. (2021) International Worm Meeting "The smallest genome in the genus Caenorhabditis"

Maeda, Yasunobu, Mehmet, Dayi, Kikuchi, Taisei, Yoshida, Akemi, Sun, Simo, Kanzaki, Natsumi

[International Worm Meeting, 2021]

Caenorhabditis elegans is a powerful laboratory model that has provided several key findings in molecular and developmental biology and neuroscience in the past decades. However, only little is known about the evolutionary history of the nematode and the relatives. Recent extensive surveys of new Caenorhabditis species around the world revealed that the diversity in the genus is bigger than we previously expected. Those resources are useful to get evolutionary insights for better understanding of biological phenomena identified in C. elegans researches and provide opportunities to perform deep evolutionary analyses on morphology, behaviors and genomes. Here we report a new Caenorhabditis species C. sp. 36, which has the smallest genome in the genus. The new gonochoristic species was isolated from a weevil (Niphades variegatus) collected in the dead log of Masson's pine in Tokyo Japan. Morphologically, the species possesses the typical characteristics of the Elegans supergroup species except the body size is a little smaller. Using Illumina, Nanopore and Hi-C technologies, we assembled the C. sp. 36 genome into six big scaffolds accounting for the chromosomes. The genome assembly size was as small as ~58Mb, the smallest among the well-defined Caenorhabditis genomes. Phylogenetic analysis revealed that C. sp. 36 is a close relative of C. japonica whose genome size is one of the biggest in the genus (156 Mb). For a comprehensive genome comparison with C. sp. 36, we also sequenced C. japonica genome using aforementioned technologies and achieved a big improvement from the wormbase ver WS279. Though the two genome sizes are different by three times, similar numbers of protein coding genes (16929 and 17652 genes, respectively) were predicted for C. sp. 36 and C. japonica, which are comparable numbers with other Caenorhabditis species. Whereas a total CDS span dose not differ much from other spices, intron and intergenic regions showed big size differences. Compared to C. elegans, C. sp. 36 has ~19.5Mb and ~18.2Mb smaller intron and intergenic spans, respectively. In contrast, those of C. japonica are ~26.3Mb and ~32.8Mb larger than of C. elegans, respectively. A deeper intron analysis revealed that although intron birth/death trends differed depending on each lineage of Caenorhabditis, each-intron length rather than per-gene intron counts mainly contribute to the intron span differences. Repeat analyses showed that transposons, especially DNA transposons are the main factors involved in the intergenic region differences.

Stevens, L. et al. (2017) International Worm Meeting "Intron loss and gain in the genus Caenorhabditis."

Blaxter, M.L., Stevens, L.

[International Worm Meeting, 2017]

The evolutionary origin of introns and the mechanisms by which they evolve remain poorly understood. In Caenorhabditis, studies of intron evolution have been restricted to a handful of taxa or single genes, and thus cannot reveal global patterns in the genus. We now have genomes for many Caenorhabditis species, generated as part of the Caenorhabditis Genomes Project (CGP) and other efforts, and this question can be revisited definitively. We developed custom software that defines orthologous introns, and applied it to genes predicted from the genomes of over 20 species of Caenorhabditis and outgroups. Placing the patterns of intron presence and absence within a phylogenetic context enabled the inference of intron gain and loss events. We show that the Caenorhabditis ancestor had substantially more introns than many present-day species, including C. elegans. Intron loss is thus a major pattern throughout Caenorhabditis evolution. We compared the characteristics of lost introns to those of retained introns to identify mechanisms responsible for this pattern. We also analyse intron gain events, which have in previous studies proved difficult to define, to identify the origins of new introns. Our findings highlight the importance of the data being produced by the CGP, allowing us to place C. elegans and the vast body of associated research within a rich evolutionary context.

Kiontke, Karin et al. (2015) International Worm Meeting "Another update on Caenorhabditis diversity, phylogeny and evolution."

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

[International Worm Meeting, 2015]

Since the 19th International C. elegans Meeting in 2013, discovery of new Caenorhabditis species has continued at a rapid rate. We now know of 63 species, 51 of which are in culture. All new species were found in tropical locations.A molecular phylogeny for 41 Caenorhabditis species was calculated with sequence data of 22 genes that were analyzed with three different algorithms. Previously reconstructed relationships within the genus are confirmed. Caenorhabditis contains three large monophyletic groups: The Drosophilae super group and the Japonica group and Elegans groups within the Elegans super group. Four species are not part of these clades and branch off early. Relationships within the Elegans super group are generally well resolved but the position of C. kamaaina remains uncertain. Two species isolated from fresh figs and likely associated with fig-wasps (Kanzaki pers. comm.) branch off as the sister group of C. elegans. The relationships within the Drosophilae super group are less well supported with conflicting placements of several subclades. We are currently incorporating the remaining species into the phylogeny.Light and scanning electron microscopic evaluation of morphology show that the diversity in phenotypic characters is large across the genus as a whole. However, most of this diversity is found in the Drosophilae super group and the basally branching species. Phenotypic diversity within the Elegans group is small in comparison. This is in contrast to the rate of molecular diversity, which is more uniform across all Caenorhabditis species. The analysis of phenotypic characters confirms that homoplasy is extensive and affects almost all characters studied.So far, genomes of 16 species have been sequenced. An initiative to sequence the genomes of all remaining Caenorhabditis species in culture was launched by Mark Blaxter and his lab in 2014 (http://caenorhabditis.bio.ed.ac.uk/).We continue to deposit morphological, biogeographical, ecological, sequence, and taxonomic data on all Caenorhabditis species in the open-access online database RhabditinaDB (http://wormtails.bio.nyu.edu/Databases). Information about Caenorhabditis isolates is also found in a WIKI on WormBase (http://evolution.wormbase.org/index.php/Main_Page).