Emmons SW et al. (1994) Worm Breeder's Gazette "Strain Names for non-C. elegans Species."

Emmons SW, Fitch DHA, Leroi AM

[Worm Breeder's Gazette, 1994]

Strain names for non-C. elegans species Scott W. Emmonst, Armand Leroit, and David Fitch, Department of Molecular Genetics, Albert Einstein College of Medicine, 1300 Morris Park Ave., Bronx, NY 10461, Department of Biology, New York University, RmlOO9 Main Bldg., Washington Square, New York, NY 10003

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

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

[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).

Miller DM et al. (1992) Worm Breeder's Gazette "unc-4 LacZ Expression in A-Type Motor Neurons"

Miller DM, Niemeyer CJ

[Worm Breeder's Gazette, 1992]

unc-4 LacZ expression in A-type motor neurons David M. Miller and Charles J. Niemeyer, Dept. of Cell Biology, Duke Univ. Medical Ctr, Durham, NC 27710

Herrera, R. Antonio et al. (2009) International Worm Meeting "Laser-Capture Microdissection and Microarray Profiling of C. elegans Male Tail Tip Morphogenesis."

Fitch, David H. A., S, Sindhoora, Herrera, R. Antonio

[International Worm Meeting, 2009]

Regulation of C. elegans male tail tip morphogenesis involves the input of several distinct molecular pathways. The heterochronic [1], Wnt signaling [2], Hox patterning [4] and sex determination [3] pathways each contribute to the proper development of the male tail tip syncytium. Mutations in certain genes result in unretracted adult male tail tips. Our lab and others have confirmed the intersection between these molecular pathways by examining the expression of transgenic reporters in various mutant backgrounds [3]. Our current understanding of the genetic network is limited, as many of these interactions are indirect. To identify candidate genes that are involved in tail tip retraction, we are performing a microarray analysis of gene expression in tail tips isolated from synchronized males and hermaphrodites prior to male L4 tail tip morphogenesis. We are using laser-capture microdissection to obtain tail tips, from which total RNA is isolated for hybridization onto Affymetrix C. elegans GeneChips. The tail tip lends itself particularly well to analysis of post-embryonic gene expression in specific somatic cells because the four tail tip cells can be removed by a single slice perpendicular to the anterior-posterior axis. Work is in progress to identify genes that are differentially expressed and/or change in expression profile from late L3 to middle L4. To confirm their role in morphogenesis, we will examine tail tip phenotypes in RNAi knockdowns or mutants of these genes. [1] Del Rio-Albrechtsen et al. 2006, Dev. Biol. 297:74. [2] Zhao et al. 2002, Development 129:1497. [3] Mason et al. 2008, Development 135:2373. [4] see MD Nelson Abstract.

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

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

[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).

Weinkove D (2018) BMC Biol "On microbes, aging and the worm: an interview with David Weinkove."

Weinkove D

[BMC Biol, 2018]

David Weinkove is an associate professor at Durham University, UK, studying host-microbe interactions in the model organism Caenorhabditis elegans. David has been focusing on the way microbes affect the physiology of their hosts, including the process of aging. In this interview, he discusses the questions shaping his research, how they evolved over the years, and his guiding principles for leading a lab.

Thomas JH et al. (1994) Worm Breeder's Gazette "lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein"

Thomas JH, Horvitz HR

[Worm Breeder's Gazette, 1994]

lin-36, a Class B Synthetic Multivulva Gene, Encodes a Novel Protein Jeffrey H. Thomas and H. Robert Horvitz, HHMI, Dept. Biology, MIT, Cambridge, MA 02139, USA

Hall DH et al. (1994) Worm Breeder's Gazette "Cytology of Degenerin-Induced Cell Death in the PVM Neuron"

Driscoll MA, Chalfie M, Gu GQ, Hall DH, Gong L

[Worm Breeder's Gazette, 1994]

Cytology of degenerin-induced cell death in the PVM neuron David H. Hall, Guoqiang Gu+, Lei Gong#, Monica Driscoll#, and Martin Chalfie+, * Dept. Neuroscience, Albert Einstein College of Medicine, Bronx, N.Y. 10461 + Dept. Biological Sciences, Columbia University, New York, N.Y. 10027 # Dept. Molecular Biology and Biochemistry, Rutgers University, Piscataway, N.J. 08855

Zarkower D et al. (1994) Worm Breeder's Gazette "mab-3 YAC Rescue"

De Bono M, Hodgkin JA, Zarkower D

[Worm Breeder's Gazette, 1994]

mab-3 YAC rescue David Zarkower, Mario de Bono, and Jonathan Hodgkin MRC Laboratory of Molecular Biology, Cambridge, England

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.