Genome Mapping and Genomics of Caenorhabditis elegans

  • Jonathan Hodgkin
  • Michael Paulini
  • Mary Ann Tuli
Part of the Genome Mapping and Genomics in Animals book series (MAPPANIMAL, volume 4)


The nematode Caenorhabditis elegans is one of the most extensively studied and utilized model organisms, owing to experimental advantages such as its ease of culture and rapid growth, facile genetics, cellular simplicity, and complete transparency throughout life. Its compact 100 Mb genome sequence was the first to be completely determined for any multicellular organism, in 1998. Early linkage mapping by recombinational methods and cytology defined a nuclear genome of five autosomes and one X (sex) chromosome, of roughly equal size. The two natural sexes are both autosomally diploid; hermaphrodites have two X chromosomes (XX) while males have one (XO). All chromosomes are holocentric, but each contains a central region where recombination is reduced and conserved house-keeping genes are more frequent. Centromeres and extended heterochromatic regions are absent. Telomeres are conventional. Annotation of the genome has defined over 20,000 protein-coding genes, with relatively few pseudogenes. About 15 % of these genes are transcribed as multicistronic operons, which are divided up into mRNAs by trans-splicing. The genome also contains many noncoding RNA genes, including a well-defined set of miRNAs. Families of transposons and repeated sequences are present but less abundant than in vertebrates. Postgenomic approaches include extensive resequencing, transcriptomics, microarray analyses and proteomics, together with determination of spatial and temporal gene expression patterns using GFP reporter transgenes, and functional testing by systematic gene deletion and global RNAi knockdown screens. Protein–protein interactions have been explored by large-scale yeast two-hybrid testing. Genome sequences for several other species within the genus Caenorhabditis have been determined; these provide a major resource for comparative genomics, and reveal a high degree of synteny between the different species.


Yeast Artificial Chromosome Spindle Microtubule Yeast Artificial Chromosome Clone Experimental Advantage Natural Race 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


  1. Barnes TM, Kohara Y, Coulson A, Hekimi S (1995) Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 141:159–179PubMedGoogle Scholar
  2. Barstead RJ, Moerman DG (2006) C. elegans deletion mutant screening. Methods Mol Biol 351:51–58PubMedGoogle Scholar
  3. Bessereau JL (2006) Transposons in C. elegans. In: WormBook.
  4. Blumenthal T (2005) Trans-splicing and operons. In: WormBook.
  5. Blumenthal T et al (2002) A global analysis of Caenorhabditis elegans operons. Nature 417:851–854PubMedCrossRefGoogle Scholar
  6. Brenner S (1974) The genetics of Caenorhabditis elegans. Genetics 77:71–94PubMedGoogle Scholar
  7. C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282:2012–2018CrossRefGoogle Scholar
  8. Chu DS, Liu H, Nix P, Wu TF, Ralston EJ, Yates JR 3rd, Meyer BJ (2006) Sperm chromatin proteomics identifies evolutionarily conserved fertility factors. Nature 443:101–115PubMedCrossRefGoogle Scholar
  9. Coulson A, Sulston J, Brenner S, Karn J (1986) Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci USA 83:7821–7825PubMedCrossRefGoogle Scholar
  10. Coulson A, Waterston R, Kiff J, Sulston J, Kohara Y (1988) Genome linking with yeast artificial chromosomes. Nature 335:184–186PubMedCrossRefGoogle Scholar
  11. Dolgin ES, Félix MA, Cutter AD (2007) Hakuna Nematoda: genetic and phenotypic diversity in African isolates of Caenorhabditis elegans and C. briggsae. Heredity 100:304–315Google Scholar
  12. Dupuy D, Bertin N, Hidalgo CA, Venkatesan K, Tu D, Lee D, Rosenberg J, Svrzikapa N, Blanc A, Carnec A, Carvunis AR, Pulak R, Shingles J, Reece-Hoyes J, Hunt-Newbury R, Viveiros R, Mohler WA, Tasan M, Roth FP, Le Peuch C, Hope IA, Johnsen R, Moerman DG, Barabási AL, Baillie D, Vidal M (2007) Genome-scale analysis of in vivo spatiotemporal promoter activity in Caenorhabditis elegans. Nat Biotechnol 25:663–668PubMedCrossRefGoogle Scholar
  13. Fire A, Xu S, Montgomery MK, Kostas SA, Driver SE, Mello CC (1998) Potent and specific genetic interference by double-stranded RNA in Caenorhabditis elegans. Nature 391:806–811PubMedCrossRefGoogle Scholar
  14. Frokjaer-Jensen C, Davis MW, Hollopeter G, Taylor J, Harris TW, Nix P, Lofgren R, Prestgard-Duke M, Bastiani M, Moerman DG, Jorgensen EM (2010) Targeted gene deletions in C. elegans using transposon excision. Nat Methods 7:451–453PubMedCrossRefGoogle Scholar
  15. Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, Koboldt DC, Waterston RH (2007) Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol 5:e167PubMedCrossRefGoogle Scholar
  16. Hunt-Newbury R, Viveiros R, Johnsen R, Mah A, Anastas D, Fang L, Halfnight E, Lee D, Lin J, Lorch A, McKay S, Okada HM, Pan J, Schulz AK, Tu D, Wong K, Zhao Z, Alexeyenko A, Burglin T, Sonnhammer E, Schnabel R, Jones SJ, Marra MA, Baillie DL, Moerman DG (2007) High-throughput in vivo analysis of gene expression in Caenorhabditis elegans. PLoS Biol 5:e237PubMedCrossRefGoogle Scholar
  17. Jones SJM, Riddle DL, Pouzyrev AT, Velculescu VE, Hillier L, Eddy SR, Stricklin SL, Baillie DL, Waterston R, Marra MA (2001) Changes in gene expression associated with developmental arrest and longevity in Caenorhabditis elegans. Genome Res 11:1346–1352PubMedCrossRefGoogle Scholar
  18. Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J (2002) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231–237CrossRefGoogle Scholar
  19. Kim SK, Lund J, Kiraly M, Duke K, Jiang M, Stuart JM, Eizinger A, Wylie BN, Davidson GS (2001) A gene expression map for Caenorhabditis elegans. Science 293:2087–2092PubMedCrossRefGoogle Scholar
  20. Kiontke K, Fitch DH (2005) The phylogenetic relationships of Caenorhabditis and other rhabditids. In: WormBook.
  21. Lee I, Lehner B, Crombie C, Wong W, Fraser AG, Marcotte EM (2008) A single gene network accurately predicts phenotypic effects of gene perturbation in Caenorhabditis elegans. Nat Genet 40:181–188PubMedCrossRefGoogle Scholar
  22. Li S et al (2004) A map of the interactome network of the metazoan C. elegans. Science 303:540–543PubMedCrossRefGoogle Scholar
  23. Luan CH, Qiu S, Finley JB, Carson M, Gray RJ, Huang W, Johnson D, Tsao J, Reboul J, Vaglio P, Hill DE, Vidal M, DeLucas LJ, Luo M (2004) High-throughput expression of C. elegans proteins. Genome Res 14:2102–2110PubMedCrossRefGoogle Scholar
  24. Maydan JS, Flibotte S, Edgley ML, Lau J, Selzer RR, Richmond TA, Pofahl NJ, Thomas JH, Moerman DG (2007) Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization. Genome Res 17:337–347PubMedCrossRefGoogle Scholar
  25. Motohashi T, Tabara H, Kohara Y (2006) Protocols for large scale in situ hybridization on C. elegans larvae. In: WormBook.
  26. Mounsey A, Bauer P, Hope IA (2002) Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes. Genome Res 12:770–775PubMedGoogle Scholar
  27. O’Rourke D, Baban D, Demidova M, Mott R, Hodgkin J (2006) Genomic clusters, putative pathogen recognition molecules, and antimicrobial genes are induced by infection of C. elegans with M. nematophilum. Genome Res 16:1005–1016PubMedCrossRefGoogle Scholar
  28. Piano F, Gunsalus KC, Hill DE, Vidal M (2006) C. elegans network biology: a beginning. In: WormBook.
  29. Putnam NH, Srivastava M, Hellsten U, Dirks B, Chapman J, Salamov A, Terry A, Shapiro H, Lindquist E, Kapitonov VV, Jurka J, Genikhovich G, Grigoriev IV, Lucas SM, Steele RE, Finnerty JR, Technau U, Martindale MQ, Rokhsar DS (2007) Sea anemone genome reveals ancestral eumetazoan gene repertoire and genomic organization. Science 317:86–94PubMedCrossRefGoogle Scholar
  30. Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207PubMedCrossRefGoogle Scholar
  31. Sanford C, Perry MD (2001) Asymmetrically distributed oligonucleotide repeats in the Caenorhabditis elegans genome sequence that map to regions important for meiotic chromosome segregation. Nucleic Acids Res 29:2920–29266PubMedCrossRefGoogle Scholar
  32. Schwarz EM (2005) Genomic classification of protein-coding gene families. In: WormBook.
  33. Stein LD et al (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1:166–192CrossRefGoogle Scholar
  34. Stewart MK, Clark NL, Merrihew G, Galloway EM, Thomas JH (2006) High genetic diversity in the chemoreceptor superfamily of Caenorhabditis elegans. Genetics 169:1985–1996CrossRefGoogle Scholar
  35. Timmons L, Court DL, Fire A (2001) Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 263:103–112PubMedCrossRefGoogle Scholar
  36. Vella MC, Slack FJ (2005) C. elegans microRNAs. In: WormBook.
  37. Zhang Y, Ma C, Delohery T, Nasipak B, Foat BC, Bounoutas A, Bussemaker HJ, Kim SK, Chalfie M (2002) Identification of genes expressed in C. elegans touch receptor neurons. Nature 418:331–335PubMedCrossRefGoogle Scholar
  38. Zhong W, Sternberg PW (2006) Genome-wide prediction of C. elegans genetic interactions. Science 311:1481–1484PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Jonathan Hodgkin
    • 1
  • Michael Paulini
    • 2
  • Mary Ann Tuli
    • 2
  1. 1.Genetics Unit, Department of BiochemistryUniversity of OxfordOxfordUK
  2. 2.Sanger Institute, The Wellcome Trust Genome CampusCambridgeUK

Personalised recommendations