Moreno SP et al. (2020) Biochem Soc Trans "Mechanisms of eukaryotic replisome disassembly."

Gambus A, Moreno SP

[Biochem Soc Trans, 2020]

DNA replication is a complex process that needs to be executed accurately before cell division in order to maintain genome integrity. DNA replication is divided into three main stages: initiation, elongation and termination. One of the key events during initiation is the assembly of the replicative helicase at origins of replication, and this mechanism has been very well described over the last decades. In the last six years however, researchers have also focused on deciphering the molecular mechanisms underlying the disassembly of the replicative helicase during termination. Similar to replisome assembly, the mechanism of replisome disassembly is strictly regulated and well conserved throughout evolution, although its complexity increases in higher eukaryotes. While budding yeast rely on just one pathway for replisome disassembly in S phase, higher eukaryotes evolved an additional mitotic pathway over and above the default S phase specific pathway. Moreover, replisome disassembly has been recently found to be a key event prior to the repair of certain DNA lesions, such as under-replicated DNA in mitosis and inter-strand cross-links (ICLs) in S phase. Although replisome disassembly in human cells has not been characterised yet, they possess all of the factors involved in these pathways in model organisms, and de-regulation of many of them are known to contribute to tumorigenesis and other pathological conditions.

Ross JL et al. (2012) J Helminthol "Diversity and distribution of nematodes associated with terrestrial slugs in the Western Cape Province of South Africa."

Ivanova ES, Wilson MJ, Ross JL, Sirgel WF, Malan AP

[J Helminthol, 2012]

A survey of nematodes associated with native and introduced species of terrestrial slugs was conducted in the Western Cape Province of South Africa, in order to gather new data regarding diversity and distribution. A total of 521 terrestrial slugs were collected from 35 localities throughout the Western Cape. All slugs were dissected and examined for the presence of internal nematodes. Extracted nematodes were identified using a combination of molecular (18S rRNA gene sequencing) and morphological techniques. Nematodes were found parasitizing slugs at 14 of the 35 sites examined, amounting to 40% of sample sites. Of all slugs, 6% were infected with nematodes. A total of seven species of nematode were identified in the province, including Agfa flexilis, Angiostoma sp., Phasmarhabditis sp. SA1, Phasmarhabditis sp. SA2, Caenorhabditis elegans, Panagrolaimus sp. and Rhabditis sp. Of these species, four were thought to be parasitic to slugs (A. flexilis, Angiostoma sp., Phasmarhabditis sp. SA1 and Phasmarhabditis sp. SA2), as opposed to forming necromenic or phoretic associations. Three new species of slug-parasitic nematode were identified during this study (Angiostoma sp., Phasmarhabditis sp. SA1 and Phasmarhabditis sp. SA2).

Kanzaki N et al. (2012) J Nematol "Two New Species of Pristionchus (Rhabditida: Diplogastridae): P. fissidentatus n. sp. from Nepal and La Reunion Island and P. elegans n. sp. from Japan."

Ragsdale EJ, Herrmann M, Kanzaki N, Sommer RJ

[J Nematol, 2012]

Pristionchus fissidentatus n. sp., isolated from soil in Nepal, and n. sp., isolated from (Coleoptera: Scarabaeidae) in Japan, are described. The two new species are recognized as basal within the genus and thus occupy an important position for macroevolutionary studies that center on the model . n. sp. is distinguished by its unique stegostomatal morphology: in the stenostomatous form, the right subventral ridge has three prominent cusps and the left subventral sector has, in addition to a plate with two cusps, a prominent denticle slightly left of ventral; in the eurystomatous form, the right subventral stegostomatal sector shows both a tooth and a ridge with several cusps. Diagnostic of n. sp. is the structure of the stenostomatous cheilostom, which bulges medially and is underlain by a large vacuolated ring. No eurystomatous form has been observed in n. sp. Reproductive modes of n. sp. and n. sp. are hermaphroditic and gonochoristic, respectively. The additional isolation of n. sp. from soil and two species of scarab beetle on La Reunion Island in the Indian Ocean suggests a broad geographic range for this species.

Wheeler D et al. (2012) J Nematol "Several Grassland Soil Nematode Species Are Insensitive to RNA-Mediated Interference."

Todd TC, Darby BJ, Herman MA, Wheeler D

[J Nematol, 2012]

Phenotypic analysis of defects caused by RNA mediated interference (RNAi) in has proven to be a powerful tool for determining gene function. In this study we investigated the effectiveness of RNAi in four non-model grassland soil nematodes, sp FVV-2., sp, sp., and sp. In contrast to reference experiments performed using and , feeding bacteria expressing dsRNA and injecting dsRNA into the gonad did not produce the expected RNAi knockdown phenotypes in any of the grassland nematodes. Quantitative reverse-transcribed PCR (qRT-PCR) assays did not detect a statistically significant reduction in the mRNA levels of endogenous genes targeted by RNAi in sp., and sp. From these studies we conclude that due to low effectiveness and inconsistent reproducibility, RNAi knockdown phenotypes in non- nematodes should be interpreted cautiously.

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.

Sudhaus W (1974) Zool. Jb. Syst. Bd. "Zur Systematik, Verbreitung, Okologie und Biologie neuer und wenig bekannter Rhabditiden (Nematoda) 2. Teil."

Sudhaus W

[Zool. Jb. Syst. Bd., 1974]

Five new species of the genus Rhabditis are described (Rh. riemanni n. sp., Rh. remanei n. sp., Rh. reciproca n. sp., Rh. blumi n. sp., and Rh. valida n. sp.) belonging to five subgenera (Crustorhabditis, Caenorhabditis, Rhabditis, Cephaloboides, and Pellioditis). The descriptions of four additional species are revised (Rh. ocypodis Chitwood, Rh. scanica Allgen, Rh. plicata Volk, and Rh. bengalensis Timm). The new subgenus Crustorhabditis n. subgen. derives from the paraphyletic subgenus Mesorhabditis. The species of the former group show a transition from living in littoral seaweed deposits to an obligate association with amphibious crabs (Crustacea). Information about the distribution, ecology, biology and ethology of all these species is presented (with two distribution maps, one for Rh. marina for comparison). Supplementary notes are given from Protorhabditis oxyuroides Sudhaus and Rhabditis tripartita von Linstow.

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.

Huang RE et al. (2014) PLoS One "Description of Caenorhabditis sinica sp. n. (Nematoda: Rhabditidae), a nematode species used in comparative biology for C. elegans."

Ren X, Zhao Z, Huang RE, Qiu Y

[PLoS One, 2014]

We re-isolated in China a relative of the nematode model Caenorhabditis elegans that was previously referred to informally as C. sp. 5. In spite of its importance for comparative biology, C. sp. 5 has remained morphologically uncharacterized. Therefore, we now provide detailed description of morphology and anatomy, assigning the name of Caenorhabditis sinica sp. n. to this nematode that is found frequently in China. C. sinica sp. n. belongs to the Elegans group in the genus Caenorhabditis, being phylogenetically close to C. briggsae although differing in reproductive mode. The gonochoristic C. sinica sp. n. displays two significantly larger distal parts of uteri filled with sperms in the female/hermaphroditic gonad than does the androdioecious C. briggsae. The new species can be differentiated morphologically from all known Caenorhabditis species within the Elegans group by presenting a uniquely shaped, three-pointed hook structure on the male precloacal lip. The lateral field of C. sinica sp. n. is marked by three ridges that are flanked by two additional incisures, sometimes appearing as five ridges in total. This study ends the prolonged period of the 'undescribed' anonymity for C. sinica sp. n. since its discovery and use in comparative biological research. Significant and crossing-direction dependent hybrid incompatibilities in F1 and F2 crossing progeny make C. sinica sp. n. an excellent model for studies of population and speciation genetics. The abundance of nematode species lacking detailed taxonomic characterization deserves renewed attention to address the species description gap for this important yet morphologically 'difficult' group of animals.