Polymorphic segmental duplication in the nematode Caenorhabditis elegans

BMC Genomics

Volumn 10, Issue , 2009, Pages

  Vergara, Ismael A ^a   Mah, Allan K ^a   Huang, Jim C ^a   Tarailo Graovac, Maja ^a   Johnsen, Robert C ^a   Baillie, David L ^a   Chen, Nansheng ^a  

^a SIMON FRASER UNIVERSITY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME 5; CONTROLLED STUDY; GENE DUPLICATION; GENE SEQUENCE; GENETIC ANALYSIS; GENETIC POLYMORPHISM; GENOTYPE; NONHUMAN; SEGMENTAL DUPLICATION; TRANSPOSON; ANIMAL; DUPLICATE GENE; GENETICS; GENOME;

CAENORHABDITIS ELEGANS;

CAENORHABDITIS ELEGANS PROTEIN;

ANIMALS; CAENORHABDITIS ELEGANS; CAENORHABDITIS ELEGANS PROTEINS; GENES, DUPLICATE; GENOME, HELMINTH; POLYMORPHISM, GENETIC;

EID: 68949216432     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-10-329     Document Type: Article

References (46)

1. Sturtevant AH The Effects of Unequal Crossing over at the Bar Locus in Drosophila Genetics 1925, 10(2):117-147 1200852 17246266
2. Bailey JA Eichler EE Primate segmental duplications: Crucibles of evolution, diversity and disease Nat Rev Genet 2006, 7(7):552-564 10.1038/nrg1895 16770338
3. Ohno S Evolution by Gene Duplication Berlin: Springer-Verlag 1970
4. Troemel ER Chou JH Dwyer ND Colbert HA Bargmann CI Divergent seven transmembrane receptors are candidate chemosensory receptors in C. elegans Cell 1995, 83(2):207-218 10.1016/0092-8674(95)90162-0 7585938
5. Robertson HM Two large families of chemoreceptor genes in the nematodes Caenorhabditis elegans and Caenorhabditis briggsae reveal extensive gene duplication, diversification, movement, and intron loss Genome Res 1998, 8(5):449-463 9582190
6. 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(2):192-203 10.1101/gr.10.2.192 10673277
7. 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(2):151-159 10.1093/chemse/ 26.2.151 11238245
8. Chen N Pai S Zhao Z Mah A Newbury R Johnsen RC Altun Z Moerman DG Baillie DL Stein LD Identification of a nematode chemosensory gene family Proc Natl Acad Sci USA 2005, 102(1):146-151 539308 15618405 10.1073/pnas.0408307102
9. Thomas JH Kelley JL Robertson HM Ly K Swanson WJ Adaptive evolution in the SRZ chemoreceptor families of Caenorhabditis elegans and Caenorhabditis briggsae Proc Natl Acad Sci USA 2005, 102(12):4476-4481 555475 15761060 10.1073/pnas.0406469102
10. Robertson HM Thomas JH The putative chemoreceptor families of C. elegans (January 06, 2006) WormBook. Edited by The C. elegans Research Community W, 2006:1-12 http://www.wormbook.org/chapters/ www_putativechemoreceptorfam/putativechemoreceptorfam.html
11. Good K Ciosk R Nance J Neves A Hill RJ Priess JR The T-box transcription factors TBX-37 and TBX-38 link GLP-1/Notch signaling to mesoderm induction in C. elegans embryos Development 2004, 131(9):1967-1978 10.1242/dev.01088 15056620
12. Zhao Z Sheps JA Ling V Fang LL Baillie DL Expression analysis of ABC transporters reveals differential functions of tandemly duplicated genes in Caenorhabditis elegans J Mol Biol 2004, 344(2):409-417 10.1016/ j.jmb.2004.09.052 15522294
13. Zhao Z Thomas JH Chen N Sheps JA Baillie DL Comparative genomics and adaptive selection of the ATP-binding-cassette gene family in caenorhabditis species Genetics 2007, 175(3):1407-1418 1840077 17194779 10.1534/genetics.106.066720
14. Thomas JH Adaptive evolution in two large families of ubiquitin-ligase adapters in nematodes and plants Genome Res 2006, 16(8):1017-1030 1524861 16825662 10.1101/gr.5089806
15. Consortium CeS Genome sequence of the nematode C. elegans: A platform for investigating biology Science 1998, 282(5396):2012-2018 10.1126/ science.282.5396.2012 9851916
16. Katju V Lynch M The structure and early evolution of recently arisen gene duplicates in the Caenorhabditis elegans genome Genetics 2003, 165(4):1793-1803 1462873 14704166
17. Hillier LW Coulson A Murray JI Bao Z Sulston JE Waterston RH Genomics in C. elegans: So many genes, such a little worm Genome Res 2005, 15(12):1651-1660 10.1101/gr.3729105 16339362
18. Zeng X Pei J Vergara IA Nesbitt MJ Wang K Chen N OrthoCluster: A new tool for mining synteny blocks and applications in comparative genomics 11th International Conference on Extending Technology (EDBT'08): 2008; Nantes, France 2008
19. Eichler EE Masquerading repeats: Paralogous pitfalls of the human genome Genome Res 1998, 8(8):758-762 9724321
20. Chen N Harris TW Antoshechkin I Bastiani C Bieri T Blasiar D Bradnam K Canaran P Chan J Chen CK et al WormBase: A comprehensive data resource for Caenorhabditis biology and genomics Nucleic Acids Res 2005, 33: Database D383-389 540020 15608221
21. Witherspoon DJ Robertson HM Neutral evolution of ten types of mariner transposons in the genomes of Caenorhabditis elegans and Caenorhabditis briggsae J Mol Evol 2003, 56(6):751-769 10.1007/s00239-002-2450-x 12911038
22. Lampe DJ Walden KK Robertson HM Loss of transposase-DNA interaction may underlie the divergence of mariner family transposable elements and the ability of more than one mariner to occupy the same genome Molecular biology and evolution 2001, 18(6):954-961
23. Brenner S The genetics of Caenorhabditis elegans Genetics 1974, 77(1):71-94 1213120 4366476
24. Riddle DL Blumenthal T Meyer BJ Priess JR Introduction to C. elegans C elegans II Cold Spring Harbor: Cold Spring Harbor Laboratory Press Riddle DL, Blumenthal T, Meyer BJ, Priess JR 1997:1-22
25. Chen N Lawson D Bradnam K Harris TW Stein LD WormBase as an integrated platform for the C. elegans ORFeome Genome Res 2004, 14(10B):2155-2161 528932 15489338 10.1101/gr.2521304
26. Kohara Y Shin-i T NEXTDB: The nematode expression pattern map database Proceedings of the International C elegans: 1999 University of Wisconsin, Madison, WI. 1999:776
27. Gilbert W The exon theory of genes Cold Spring Harb Symp Quant Biol 1987, 52:901-905 2456887
28. Katju V Lynch M On the formation of novel genes by duplication in the Caenorhabditis elegans genome Molecular biology and evolution 2006, 23(5):1056-1067 10.1093/molbev/msj114
29. Semple C Wolfe KH Gene duplication and gene conversion in the Caenorhabditis elegans genome Journal of molecular evolution 1999, 48(5):555-564 10.1007/PL00006498 10198121
30. Friedman R Hughes AL Pattern and timing of gene duplication in animal genomes Genome research 2001, 11(11):1842-1847 311158 11691848
31. Friedman R Hughes AL Gene duplication and the structure of eukaryotic genomes Genome research 2001, 11(3):373-381 311031 11230161 10.1101/ gr.155801
32. Cavalcanti AR Ferreira R Gu Z Li WH Patterns of gene duplication in Saccharomyces cerevisiae and Caenorhabditis elegans Journal of molecular evolution 2003, 56(1):28-37 10.1007/s00239-002-2377-2 12569420
33. Clark DV Johnsen RC McKim KS Baillie DL Analysis of lethal mutations in a mutator strain that activates transposable elements in Caenorhabditis elegans Genome 1990, 33(1):109-114 2158925
34. Jensen VL Albert PS Riddle DL Caenorhabditis elegans SDF-9 enhances insulin/insulin-like signaling through interaction with DAF-2 Genetics 2007, 177(1):661-666 2013707 17660545 10.1534/genetics.107.076703
35. Riddle DL Blumenthal T Meyer BJ Priess JR Introduction to C. elegans - Origins of the Model C elegans II CSHL Press: USA 1997
36. Bargmann CI Chemosensation in C. elegans (October 25, 2006) WormBook. Edited by The C. elegans Research Community W, 2006:1-29 http://wormbook.org/chapters/www_chemosensation/chemosensation.html
37. Wicks SR Yeh RT Gish WR Waterston RH Plasterk RH Rapid gene mapping in Caenorhabditis elegans using a high density polymorphism map Nature genetics 2001, 28(2):160-164 10.1038/88878 11381264
38. Maydan JS Flibotte S Edgley ML Lau J Selzer RR Richmond TA Pofahl NJ Thomas JH Moerman DG Efficient high-resolution deletion discovery in Caenorhabditis elegans by array comparative genomic hybridization Genome Res 2007, 17(3):337-347 1800925 17267812 10.1101/gr.5690307
39. Hillier LW Marth GT Quinlan AR Dooling D Fewell G Barnett D Fox P Glasscock JI Hickenbotham M Huang W et al Whole-genome sequencing and variant discovery in C. elegans Nature methods 2008, 5(2):183-188 10.1038/nmeth.1179 18204455
40. Sarin S Prabhu S O'Meara MM Pe'er I Hobert O Caenorhabditis elegans mutant allele identification by whole-genome sequencing Nature methods 2008, 5(10):865-867 10.1038/nmeth.1249 18677319
41. Altschul SF Madden TL Schaffer AA Zhang J Zhang Z Miller W Lipman DJ Gapped BLAST and PSI-BLAST: A new generation of protein database search programs Nucleic Acids Res 1997, 25(17):3389-3402 146917 9254694 10.1093/ nar/25.17.3389
42. Thompson JD Higgins DG Gibson TJ CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice Nucleic Acids Res 1994, 22(22):4673-4680 308517 7984417 10.1093/nar/22.22.4673
43. Birney E Durbin R Using GeneWise in the Drosophila annotation experiment Genome Res 2000, 10(4):547-548 310858 10779496 10.1101/gr.10.4.547
44. Birney E Clamp M Durbin R GeneWise and Genomewise Genome Res 2004, 14(5):988-995 479130 15123596 10.1101/gr.1865504
45. Jurka J Repbase update: A database and an electronic journal of repetitive elements Trends Genet 2000, 16(9):418-420 10.1016/ S0168-9525(00)02093-X 10973072
46. Barstead RJ Kleiman L Waterston RH Cloning, sequencing, and mapping of an alpha-actinin gene from the nematode Caenorhabditis elegans Cell Motil Cytoskeleton 1991, 20(1):69-78 10.1002/cm.970200108 1756579