Genome evolution in Caenorhabditis

Briefings in Functional Genomics and Proteomics

Volumn 7, Issue 3, 2008, Pages 211-216

  Thomas, James H ^a  

^a UNIVERSITY OF WASHINGTON   (United States)

Author keywords

Caenorhabditis; Evolution; Gene function; Genome; Population diversity

Indexed keywords

BASIC HELIX LOOP HELIX TRANSCRIPTION FACTOR; BASIC LEUCINE ZIPPER TRANSCRIPTION FACTOR; HIGH MOBILITY GROUP PROTEIN; PROTEIN MYB; RNA; T BOX TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ETS; ZINC FINGER PROTEIN;

ARTICLE; BRUGIA MALAYI; CAENORHABDITIS; CAENORHABDITIS BRENNERI; CAENORHABDITIS BRIGGSA; CAENORHABDITIS ELEGANS; CAENORHABDITIS JAPONICA; CAENORHABDITIS REMANEI; CHEMOSENSITIZATION; GENE FUNCTION; GENE LOCATION; GENE NUMBER; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAEMONCHUS CONTORTUS; KNOCKOUT GENE; MOLECULAR EVOLUTION; MULTIGENE FAMILY; NEMATODE; NONHUMAN; ORTHOLOGY; PHENOTYPE; POPULATION GENETICS; PRISTIONCHUS PACIFICUS; PROTEIN ANALYSIS; RNA GENE; RNA INTERFERENCE; SPECIES COMPARISON; SPECIES DIFFERENTIATION; TRICHINELLA SPIRALIS; XENOBIOTIC METABOLISM;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; EVOLUTION, MOLECULAR; GENES, HELMINTH; GENOME, HELMINTH; VARIATION (GENETICS);

BRUGIA MALAYI; CAENORHABDITIS; CAENORHABDITIS BRIGGSAE; CAENORHABDITIS ELEGANS; CAENORHABDITIS JAPONICA; CAENORHABDITIS REMANEI; HAEMONCHUS CONTORTUS; HEXAPODA; MAMMALIA; METAZOA; NEMATODA; PRISTIONCHUS PACIFICUS; TRICHINELLA SPIRALIS;

EID: 48949116734     PISSN: 14739550     EISSN: 14774062     Source Type: Journal    
DOI: 10.1093/bfgp/eln022     Document Type: Article

References (54)

1. The C. elegans Consortium. Genome sequence of the nematode C. elegans: A platform for investigating biology. The C elegans Sequencing Consortium. Science 1998;282:2012-8.
2. Clark AG, Eisen MB, Smith DR, et al. Evolution of genes and genomes on the Drosophila phylogeny. Nature 2007;450: 203-18.
3. Clamp M, Fry B, Kamal M, et al. Distinguishing protein-coding and noncoding genes in the human genome. Proc Natl Acad Sci USA 2007;104:19428-33.
4. Kiontke K, Gavin NP, Raynes Y, et al. Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sci USA 2004;101: 9003-8.
5. Cho S, Jin SW, Cohen A, et al. A phylogeny of Caenorhabditis reveals frequent loss of introns during nematode evolution. Genome Res 2004;14:1207-20.
6. Denver DR, Morris K, Lynch M, et al. High mutation rate and predominance of insertions in the Caenorhabditis elegans nuclear genome. Nature 2004;430:679-82.
7. Cutter AD. Divergence times in Caenorhabditis and Drosophila inferred from direct estimates of the neutral mutation rate. Mol Biol Evol 2008;25:778-86.
8. Stein LD, Bao Z, Blasiar D, et al. The genome sequence of Caenorhabditis briggsae: A plafform for comparative genomics. PLoS Biol 2003;1:E45.
9. Felix MA. Genomes: A helpfid cousin for our favourite worm. Curr Biol 2004;14:R75-7.
10. Borneman AR, Gianoulis TA, Zhang ZD, et al. Divergence of transcription factor binding sites across related yeast species. Science 2007;317:815-9.
11. Hahn MW, Demuth JP, Han SG. Accelerated rate of gene gain and loss in primates. Genetics 2007;177:1941-9.
12. Gibbs RA, Rogers J, Katze MG, et al. Evolutionary and biomedical insights from the rhesus macaque genome. Science 2007;316 222-34.
13. Siepel A, Bejerano G, Pedersen JS, et al. Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res 2005;15:1034-50.
14. Kabat JL, Barberan-Soler S, McKenna P, et al. Intronic alternative splicing regulators identified by comparative genomics in nematodes. PLoS Comput Biol 2006;2:e86.
15. Castillo-Davis CI, Hartl DL. Genorne evolution and developmental constraint in Caenorhabditis elegans. Mol Biol Evol 2002;19 728-35.
16. Cutter AD, Charlesworth B. Selection intensity on preferred codons correlates with overall codon usage bias in Caenorhabdids remanei. Curr Biol 2006;16:2053-7.
17. Duret L, Mouchiroud D. Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci USA 1999;96: 4482-7.
18. Hillier LW, Miller RD, Baird SE, et al. Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol 2007;5:e167.
19. Ghedin E, Wang S, Spiro D, et al. Draft genome of the filarial nematode parasite Brugia malayi. Science 2007;317: 1756-60.
20. Robertson HM, Thomas JH. The putative chemoreceptor gene families. In: WormBook, The C. elegans Research Community. http://www.wormbook.org/chapters/www_putativechemoreceptorfam/ putativechemoreceptorfam. html (2 June 2008, date last accessed).
21. Robertson HM. The, large SRH family of chemoreceptor genes in Caenorhabditis nematodes reveals processes of genome evolution involving large duplications and deletions and intron gains and losses. Genome Res. 2000;10: 192-203.
22. Robertson HM. Updating the STR and SRJ (STL) families of chemoreceptors in Caenorhabditis nematodes reveals frequent gene movement within and between chromosomes. Chem Senses 2001;26:151-9.
23. Thomas JH, Kelley JL, Robertson HM, et al. Adaptive evolution in the SRZ chomoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae. Proc Natl Acad Sci USA 2005;102 4476-81.
24. Salkoff L, Wei AD, Baban B, et al. Potassium channels in C elegans. In: WormBook, The C. elegans Research Community. http://www.wormbook.org/chapters/www_function/function.html (2 June 2008, date last accessed).
25. Thomas JH. Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants. Genome Res 2006;16:1017-30.
26. Robinson-Rechavi M, Maina CV, Gissendanner CR, et al. Explosive lineage-specific expansion of the orphan nuclear receptor HNF4 in nematodes. J Mol Evol 2005;60: 577-86.
27. Van Gilst M, Gissendanner CR, Sluder AE. Diversity and function of orphan nuclear receptors in nematodes. Crit Rev Eukaryot Gene Expr 2002;12:65-88.
28. Sluder AE, Maina CV. Nuclear receptors in nematodes: Themes and variations. Trends Genet 2001;17:206-13.
29. Fitzpatrick DA, O'Halloran DM, Burnell AM. Multiple lineage specific expansions within the guanylyl cyclase gene family. BMC Evol Biol 2006;6:26.
30. O'Halloran DM, Fitzpatrick DA, McCormack GP, et al. The molecular phylogeny of a nematode-specific clade of heterotrimeric G-protein alpha-subunit genes. J Mol Evol 2006;63:87-94.
31. Dillon J, Hopper NA, Holden-Dye L, et al. Molecular characterization of the metabotropic glutamate receptor family in Caenorhabditis elegans. Biochem Soc Trans 2006;34: 942-8.
32. Zhao Z, Thomas JH, Chen N, et al. Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in Caenorhabditis species. Genetics 2007;175: 1407-18.
33. Brenner S. The genetics of Caenorhabditis elegans. Genetics 1974;77:71-94.
34. Barnes TM, Kohara Y, Coulson A, et al. Meiotic recombination, noncoding DNA and genomic organization in Caenorhabditis elegans. Genetics 1995;141:159-79.
35. Kamath RS, Fraser AG, Dong Y, et al. Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 2003;421:231-7.
36. Thomas JH. Analysis of homologous gene clusters in Caenorhabditis elegans reveals striking regional cluster domains. Genetics 2006;172:127-43.
37. Koch R, van Luenen HG, van der Horst M, et al. Single nucleotide polymorphisms in wild isolates of Caenorhabditis elegans. Genome Res 2000;10:1690-6.
38. Wicks SR, Yeh RT, Gish WR, et al. Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map. Nat Genet 2001;28:160-4.
39. Maydan JS, Flibotte S, Edgley ML, et al. Efficient high-resolution deletion discovery in Caenorhabdsitiseℓgans by array comparative genomic hybridization. Genome Res 2007; 17: 337-47.
40. Reece-Hoyes JS, Deplancke B, Shingles J, et al. A compendium of Caenorhabditis elegans regulatory transcription factors: A resource for mapping transcription regulatory networks. Genome Biol 2005; 6:R110.
41. Maglich JM, Sluder A, Guan X, et al. Comparison of complete nuclear receptor sets from the human, Caenorhabditis elegans and Drosophila genomes. Genome Biol 2001;2:RESEARCH0029.
42. Sluder AE, Mathews SW, Hough D, et al. The nuclear receptor superfamily has undergone extensive proliferation and diversification in nematodes. Genome Res 1999;9: 103-20.
43. Timmons L, Court DL, Fire A. Ingestion of bacterially expressed dsRNAs can produce specific and potent genetic interference in Caenorhabditis elegans. Gene 2001;263: 103-12.
44. Kamath RS, Martinez-Campos M, Zipperlen P, et al. Effectiveness of specific RNA-mediated interference through ingested double-stranded RNA in Caenorhabditis elegans. Genome Biol 2001;2:RESEARCH0002.
45. Kamath RS, Ahringer J. Genome-wide RNAi screening in Caenorhabditis elegans. Methods 2003;30:313-21.
46. Barriere A, Felix MA. High local genetic diversity and low outcrossing rate in Caenorhabditis elegans natural populations. Curr Biol 2005;15:1176-84.
47. Cutter AD. Nucleotide polymorphism and linkage dis-equilibrium in wild populations of the partial selfer Caenorhabditis elegans. Genetics 2006;172:171-84.
48. Cutter AD, Baird SE, Charlesworth D. High nucleotide polymorphism and rapid decay of linkage disequilibrium in wild populations of Caenorhabditis remanei. Genetics 2006;174: 901-13.
49. Cutter AD. Multilocus patterns of polymorphism and selection across the X chromosome of Caenorhabditis remanei. Genetics 2008;178 1661-72.
50. Graustein A, Gaspar JM, Walters JR, et al. Levels of DNA polymorphism vary with mating system in the nematode genus Caenorhabditis. Genetics 2002;161:99-107.
51. Barriere A, Felix MA. Temporal dynamics and linkage disequilibrium in natural Caenorhabditis elegans populations. Genetics 2007; 176:999-1011.
52. Sivasundar A, Hey J. Sampling from natural populations with RNAI reveals high outcrossing and population structure in Caenorhabditis elegans. Curr Biol 2005;15: 1598-602.
53. Sivasundar A, Hey J. Population genetics of Caenorhabditis elegans the paradox of low polymorphism in a widespread species. Genetics 2003;163:147-57.
54. Hillier LW, Marth GT, Quinlan AR, et al. Whole-genome sequencing and variant discovery in C. elegans. Nat Methods 2008;5 183-8.