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Genetics. Sep 1995; 141(1): 159–179.
PMCID: PMC1206715

Meiotic Recombination, Noncoding DNA and Genomic Organization in Caenorhabditis Elegans


The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.
  • Albertson DG, Thomson JN. The kinetochores of Caenorhabditis elegans. Chromosoma. 1982;86(3):409–428. [PubMed]
  • Bernardi G. The isochore organization of the human genome and its evolutionary history--a review. Gene. 1993 Dec 15;135(1-2):57–66. [PubMed]
  • Cangiano G, La Volpe A. Repetitive DNA sequences located in the terminal portion of the Caenorhabditis elegans chromosomes. Nucleic Acids Res. 1993 Mar 11;21(5):1133–1139. [PMC free article] [PubMed]
  • Chakravarti A. A graphical representation of genetic and physical maps: the Marey map. Genomics. 1991 Sep;11(1):219–222. [PubMed]
  • Charlesworth B, Langley CH, Stephan W. The evolution of restricted recombination and the accumulation of repeated DNA sequences. Genetics. 1986 Apr;112(4):947–962. [PMC free article] [PubMed]
  • Charlesworth B, Morgan MT, Charlesworth D. The effect of deleterious mutations on neutral molecular variation. Genetics. 1993 Aug;134(4):1289–1303. [PMC free article] [PubMed]
  • Chuang PT, Albertson DG, Meyer BJ. DPY-27:a chromosome condensation protein homolog that regulates C. elegans dosage compensation through association with the X chromosome. Cell. 1994 Nov 4;79(3):459–474. [PubMed]
  • Civardi L, Xia Y, Edwards KJ, Schnable PS, Nikolau BJ. The relationship between genetic and physical distances in the cloned a1-sh2 interval of the Zea mays L. genome. Proc Natl Acad Sci U S A. 1994 Aug 16;91(17):8268–8272. [PMC free article] [PubMed]
  • Coulson A, Sulston J, Brenner S, Karn J. Toward a physical map of the genome of the nematode Caenorhabditis elegans. Proc Natl Acad Sci U S A. 1986 Oct;83(20):7821–7825. [PMC free article] [PubMed]
  • de Lange T. Human telomeres are attached to the nuclear matrix. EMBO J. 1992 Feb;11(2):717–724. [PMC free article] [PubMed]
  • Dujon B, Alexandraki D, André B, Ansorge W, Baladron V, Ballesta JP, Banrevi A, Bolle PA, Bolotin-Fukuhara M, Bossier P, et al. Complete DNA sequence of yeast chromosome XI. Nature. 1994 Jun 2;369(6479):371–378. [PubMed]
  • Emmons SW, Rosenzweig B, Hirsh D. Arrangement of repeated sequences in the DNA of the nematode Caenorhabditis elegans. J Mol Biol. 1980 Dec 25;144(4):481–500. [PubMed]
  • Felsenstein KM, Emmons SW. Nematode repetitive DNA with ARS and segregation function in Saccharomyces cerevisiae. Mol Cell Biol. 1988 Feb;8(2):875–883. [PMC free article] [PubMed]
  • Gibson TJ, Rosenthal A, Waterston RH. Lorist6, a cosmid vector with BamHI, NotI, ScaI and HindIII cloning sites and altered neomycin phosphotransferase gene expression. Gene. 1987;53(2-3):283–286. [PubMed]
  • Greenwald I, Coulson A, Sulston J, Priess J. Correlation of the physical and genetic maps in the lin-12 region of Caenorhabditis elegans. Nucleic Acids Res. 1987 Mar 11;15(5):2295–2307. [PMC free article] [PubMed]
  • Herman RK, Kari CK. Recombination between small X chromosome duplications and the X chromosome in Caenorhabditis elegans. Genetics. 1989 Apr;121(4):723–737. [PMC free article] [PubMed]
  • Herman RK, Kari CK, Hartman PS. Dominant X-chromosome nondisjunction mutants of Caenorhabditis elegans. Genetics. 1982 Nov;102(3):379–400. [PMC free article] [PubMed]
  • Hodgkin J, Horvitz HR, Brenner S. Nondisjunction Mutants of the Nematode CAENORHABDITIS ELEGANS. Genetics. 1979 Jan;91(1):67–94. [PMC free article] [PubMed]
  • Ikemura T, Wada K. Evident diversity of codon usage patterns of human genes with respect to chromosome banding patterns and chromosome numbers; relation between nucleotide sequence data and cytogenetic data. Nucleic Acids Res. 1991 Aug 25;19(16):4333–4339. [PMC free article] [PubMed]
  • Johnston M, Andrews S, Brinkman R, Cooper J, Ding H, Dover J, Du Z, Favello A, Fulton L, Gattung S, et al. Complete nucleotide sequence of Saccharomyces cerevisiae chromosome VIII. Science. 1994 Sep 30;265(5181):2077–2082. [PubMed]
  • Kaplan NL, Hudson RR, Langley CH. The "hitchhiking effect" revisited. Genetics. 1989 Dec;123(4):887–899. [PMC free article] [PubMed]
  • Kennedy BP, Aamodt EJ, Allen FL, Chung MA, Heschl MF, McGhee JD. The gut esterase gene (ges-1) from the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Mol Biol. 1993 Feb 20;229(4):890–908. [PubMed]
  • La Volpe A, Ciaramella M, Bazzicalupo P. Structure, evolution and properties of a novel repetitive DNA family in Caenorhabditis elegans. Nucleic Acids Res. 1988 Sep 12;16(17):8213–8231. [PMC free article] [PubMed]
  • Madl JE, Herman RK. Polyploids and sex determination in Caenorhabditis elegans. Genetics. 1979 Oct;93(2):393–402. [PMC free article] [PubMed]
  • Smith JM, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res. 1974 Feb;23(1):23–35. [PubMed]
  • McKim KS, Howell AM, Rose AM. The effects of translocations on recombination frequency in Caenorhabditis elegans. Genetics. 1988 Dec;120(4):987–1001. [PMC free article] [PubMed]
  • McKim KS, Peters K, Rose AM. Two types of sites required for meiotic chromosome pairing in Caenorhabditis elegans. Genetics. 1993 Jul;134(3):749–768. [PMC free article] [PubMed]
  • Meyer BJ, Casson LP. Caenorhabditis elegans compensates for the difference in X chromosome dosage between the sexes by regulating transcript levels. Cell. 1986 Dec 26;47(6):871–881. [PubMed]
  • Mouchiroud D, D'Onofrio G, Aïssani B, Macaya G, Gautier C, Bernardi G. The distribution of genes in the human genome. Gene. 1991 Apr;100:181–187. [PubMed]
  • Oliver SG, van der Aart QJ, Agostoni-Carbone ML, Aigle M, Alberghina L, Alexandraki D, Antoine G, Anwar R, Ballesta JP, Benit P, et al. The complete DNA sequence of yeast chromosome III. Nature. 1992 May 7;357(6373):38–46. [PubMed]
  • Prasad SS, Baillie DL. Evolutionarily conserved coding sequences in the dpy-20-unc-22 region of Caenorhabditis elegans. Genomics. 1989 Aug;5(2):185–198. [PubMed]
  • Rosenbluth RE, Baillie DL. The genetic analysis of a reciprocal translocation, eT1(III; V), in Caenorhabditis elegans. Genetics. 1981 Nov-Dec;99(3-4):415–428. [PMC free article] [PubMed]
  • Sigurdson DC, Herman RK, Horton CA, Kari CK, Pratt SE. An X-autosome fusion chromosome of Caenorhabditis elegans. Mol Gen Genet. 1986 Feb;202(2):212–218. [PubMed]
  • Starr T, Howell AM, McDowall J, Peters K, Rose AM. Isolation and mapping of DNA probes within the linkage group I gene cluster of Caenorhabditis elegans. Genome. 1989 Jun;32(3):365–372. [PubMed]
  • Stephan W. Recombination and the evolution of satellite DNA. Genet Res. 1986 Jun;47(3):167–174. [PubMed]
  • Sulston J, Du Z, Thomas K, Wilson R, Hillier L, Staden R, Halloran N, Green P, Thierry-Mieg J, Qiu L, et al. The C. elegans genome sequencing project: a beginning. Nature. 1992 Mar 5;356(6364):37–41. [PubMed]
  • Waterston R, Martin C, Craxton M, Huynh C, Coulson A, Hillier L, Durbin R, Green P, Shownkeen R, Halloran N, et al. A survey of expressed genes in Caenorhabditis elegans. Nat Genet. 1992 May;1(2):114–123. [PubMed]
  • Wilson R, Ainscough R, Anderson K, Baynes C, Berks M, Bonfield J, Burton J, Connell M, Copsey T, Cooper J, et al. 2.2 Mb of contiguous nucleotide sequence from chromosome III of C. elegans. Nature. 1994 Mar 3;368(6466):32–38. [PubMed]
  • Wu TC, Lichten M. Meiosis-induced double-strand break sites determined by yeast chromatin structure. Science. 1994 Jan 28;263(5146):515–518. [PubMed]
  • Zetka MC, Rose AM. Sex-related differences in crossing over in Caenorhabditis elegans. Genetics. 1990 Oct;126(2):355–363. [PMC free article] [PubMed]

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