Lunt, David H. et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "COMPARATIVE GENOMICS OF ROOT KNOT NEMATODES: TALES OF SEX, HYBRIDISATION"

Lunt, David H., Blaxter, Mark L., Kumar, Sujai, Koutsovoulos, Georgios

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Root knot nematodes (RKN) can infect most of the world's agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of this extreme polyphagy. It has been suggested that the most damaging pathogens have originated from interspecific hybridizations between unknown parental taxa. We have sequenced the genome of Meloidogyne floridensis, and use comparative evolutionary genomics of RKN to test the hypothesis that this species was involved in the hybrid origin of the agriculturally important species Meloidogyne incognita. Phylogenomic analyses of gene families indicate that RKN species may have very complex origins involving the mixing of several parental genomes by hybridization. The extreme polyphagy of some RKN, and their success in agricultural environments, may be related to this hybridisation, producing transgressive variation on which natural selection can act. This comparative genomic analysis provides a compelling example of the importance and complexity of hybridization in generating animal species diversity more generally.

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

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.

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

Blaxter, Mark et al. (2021) International Worm Meeting "A catalogue of nematode karyotypes"

Leech, Chloe, Lunt, David, Blaxter, Mark

[International Worm Meeting, 2021]

Observation of the behaviour of nematode chromosomes during meiosis by Boveri was critical to the development of the germline theory of inheritance in the late 19th century. In the current era of genomics, knowledge of the karyotype of a species is very useful in conditioning expectations of the assembly. Caenorhabditis elegans has six chromosomes, comprising five autosomes and an X. Other Caenorhabditis species also have six chromosomes, but in the sister group to Caenorhabditis, the Protorhabditis-Diploscapter clade, chromosome numbers range from 6 to 1. These changes in chromosome number imply changes in gene linkage, and also therefore in gene coregulation. Previous catalogues of nematode chromosome numbers were limited in scope (for example including data from only plant parasites or only animal parasites) or contain species names that are no longer current. We have collated a catalogue of chromosome numbers, and sex determination karyotypes, from literature from 1883 to the present day. We identified the current names for species described in older literature, and placed these data in a modern taxonomy. We identified chromosome counts for 218 species from 95 genera in 44 families. As is often the case in Nematoda, free-living species from non-rhabditid Chromadoria, Enoplia and Dorylaimia are poorly represented, Haploid chromosome numbers range from 1 to over 50, with variability especially in the plant parasitic Meloidogyninae. The modal reported haploid chromosome number is 6. Sex determination mechanisms, derived from karyotypic differences between males and females, and between different spermatid nuclei, are commonly XX-XO with several independent origins of XX-XY systems. Ascaridomorpha includes many species with multiple X chromosomes. Many nematodes are parthenogens, and parthenogenesis is associated in some lineages with polyploidy (triploidy and tetraploidy). The catalogue is available via the Genomes on a Tree system (https://goat.genomehubs.org/preview).

Grenache DG et al. (1993) Worm Breeder's Gazette "Differential Effects of Dauer-Defective Mutations in L1-Specific Surface Antigen Switching"

Politz SM, Grenache DG

[Worm Breeder's Gazette, 1993]

DIFFERENTIAL EFFECTS OF DAUER-DEFECTIVE MUTATIONS ON L1- SPECIFIC SURFACE ANTIGEN SWITCHING. David G. Grenache and Samuel M. Politz, Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA.

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

Szitenberg, Amir et al. (2014) Evolutionary Biology of Caenorhabditis and Other Nematodes "THE EVOLUTION OF TYROSINE-RECOMBINASE ELEMENTS IN NEMATODA"

Blaxter, Mark L, Szitenberg, Amir, Lunt, David H, Koutsovoulos, Georgios

[Evolutionary Biology of Caenorhabditis and Other Nematodes, 2014]

Transposable elements can be categorised into DNA and RNA elements based on their mechanism of transposition. Tyrosine recombinase elements (YREs) are relatively rare and poorly understood, despite sharing characteristics with both DNA and RNA elements. Previously, the Nematoda have been reported to have a substantially different diversity of YREs compared to other animal phyla: the Dirs1-like YRE retrotransposon was encountered in most animal phyla but not in Nematoda, and a unique Pat1-like YRE retrotransposon has only been recorded from Nematoda. We explored the diversity of YREs in Nematoda by sampling broadly across the phylum and including 34 genomes representing the three classes within Nematoda. We developed a method to isolate and classify YREs based on both feature organization and phylogenetic relationships in an open and reproducible workflow. We also ensured that our phylogenetic approach to YRE classification identified truncated and degenerate elements, informatively increasing the number of elements sampled. We identified Dirs1-like elements (thought to be absent from Nematoda) in the nematode classes Enoplia and Dorylaimia indicating that nematode model species do not adequately represent the diversity of transposable elements in the phylum. Nematode Pat1- like elements were found to be a derived form of another PAT element that is present more widely in animals. Several sequence features used widely for the classification of YREs were found to be homoplasious, highlighting the need for a phylogenetically-based classification scheme. Nematode model species do not represent the diversity of transposable elements in the phylum.

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

Amrit FRG et al. (2017) J Vis Exp "Transcriptomic Analysis of C. elegans RNA Sequencing Data Through the Tuxedo Suite on the Galaxy Project."

Ghazi A, Amrit FRG

[J Vis Exp, 2017]

Next generation sequencing (NGS) technologies have revolutionized the nature of biological investigation. Of these, RNA Sequencing (RNA-Seq) has emerged as a powerful tool for gene-expression analysis and transcriptome mapping. However, handling RNA-Seq datasets requires sophisticated computational expertise and poses inherent challenges for biology researchers. This bottleneck has been mitigated by the open access Galaxy project that allows users without bioinformatics skills to analyze RNA-Seq data, and the Database for Annotation, Visualization, and Integrated Discovery (DAVID), a Gene Ontology (GO) term analysis suite that helps derive biological meaning from large data sets. However, for first-time users and bioinformatics' amateurs, self-learning and familiarization with these platforms can be time-consuming and daunting. We describe a straightforward workflow that will help C. elegans researchers to isolate worm RNA, conduct an RNA-Seq experiment and analyze the data using Galaxy and DAVID platforms. This protocol provides stepwise instructions for using the various Galaxy modules for accessing raw NGS data, quality-control checks, alignment, and differential gene expression analysis, guiding the user with parameters at every step to generate a gene list that can be screened for enrichment of gene classes or biological processes using DAVID. Overall, we anticipate that this article will provide information to C. elegans researchers undertaking RNA-Seq experiments for the first time as well as frequent users running a small number of samples.