Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes
10.1186/gb-2002-3-10-research0057
Crossref journal-article
Springer Science and Business Media LLC
Genome Biology (297)
Bibliography

Guiliano, D., Hall, N., Jones, S., Clark, L., Corton, C., Barrell, B., & Blaxter, M. (2002). Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biology, 3(10).

Authors 7
  1. DB Guiliano (first)
  2. N Hall (additional)
  3. SJM Jones (additional)
  4. LN Clark (additional)
  5. CH Corton (additional)
  6. BG Barrell (additional)
  7. ML Blaxter (additional)
References 61 Referenced 37
  1. Hentschel CC, Birnstiel ML: The organization and expression of histone gene families. Cell. 1981, 25: 301-313. (10.1016/0092-8674(81)90048-9) / Cell by CC Hentschel (1981)
  2. Ferrier DE, Holland PW: Ancient origin of the Hox gene cluster. Nat Rev Genet. 2001, 2: 33-38. 10.1038/35047605. (10.1038/35047605) / Nat Rev Genet by DE Ferrier (2001)
  3. Litman GW, Rast JP, Shamblott MJ, Haire RN, Hulst M, Roess W, Litman RT, Hinds-Frey KR, Zilch A, Amemiya CT: Phylogenetic diversification of immunoglobulin genes and the antibody repertoire. Mol Biol Evol. 1993, 10: 60-72. / Mol Biol Evol by GW Litman (1993)
  4. Ohta Y, Okamura K, McKinney EC, Bartl S, Hashimoto K, Flajnik MF: Primitive synteny of vertebrate major histocompatibility complex class I and class II genes. Proc Natl Acad Sci USA. 2000, 97: 4712-4717. 10.1073/pnas.97.9.4712. (10.1073/pnas.97.9.4712) / Proc Natl Acad Sci USA by Y Ohta (2000)
  5. Ranz JM, Casals F, Ruiz A: How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res. 2001, 11: 230-239. 10.1101/gr.162901. (10.1101/gr.162901) / Genome Res by JM Ranz (2001)
  6. Coghlan A, Wolfe KH: Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res. 2002, 12: 857-867. 10.1101/gr.172702. (10.1101/gr.172702) / Genome Res by A Coghlan (2002)
  7. O'Brien SJ, Menotti-Raymond M, Murphy WJ, Nash WG, Wienberg J, Stanyon R, Copeland NG, Jenkins NA, Womack JE, Marshall Graves JA: The promise of comparative genomics in mammals. Science. 1999, 286: 458-462. 10.1126/science.286.5439.458. (10.1126/science.286.5439.458) / Science by SJ O'Brien (1999)
  8. Fulton RE, Salasek ML, DuTeau NM, Black WCT: SSCP analysis of cDNA markers provides a dense linkage map of the Aedes aegypti genome. Genetics. 2001, 158: 715-726. (10.1093/genetics/158.2.715) / Genetics by RE Fulton (2001)
  9. Kent WJ, Zahler AM: Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res. 2000, 10: 1115-1125. 10.1101/gr.10.8.1115. (10.1101/gr.10.8.1115) / Genome Res by WJ Kent (2000)
  10. Caceres M, Ranz JM, Barbadilla A, Long M, Ruiz A: Generation of a widespread Drosophila inversion by a transposable element. Science. 1999, 285: 415-418. 10.1126/science.285.5426.415. (10.1126/science.285.5426.415) / Science by M Caceres (1999)
  11. Caceres M, Puig M, Ruiz A: Molecular characterization of two natural hotspots in the Drosophila buzzatii genome induced by transposon insertions. Genome Res. 2001, 11: 1353-1364. 10.1101/gr.174001. (10.1101/gr.174001) / Genome Res by M Caceres (2001)
  12. Thomas WK, Wilson AC: Mode and tempo of molecular evolution in the nematode caenorhabditis: cytochrome oxidase II and calmodulin sequences. Genetics. 1991, 128: 269-279. (10.1093/genetics/128.2.269) / Genetics by WK Thomas (1991)
  13. The C. elegans Sequencing Consortium: Genome sequence of the nematode C. elegans: a platform for investigating biology. Science. 1998, 282: 2012-2018. 10.1126/science.282.5396.2012. (10.1126/science.282.5396.2012) / Science by The C. elegans Sequencing Consortium (1998)
  14. Vanfleteren JR, Van de Peer Y, Blaxter ML, Tweedie SA, Trotman C, Lu L, Van Hauwaert ML, Moens L: Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences. Mol Phylogenet Evol. 1994, 3: 92-101. 10.1006/mpev.1994.1012. (10.1006/mpev.1994.1012) / Mol Phylogenet Evol by JR Vanfleteren (1994)
  15. McReynolds LA, DeSimone SM, Williams SA: Cloning and comparison of repeated DNA sequences from the human filarial parasite Brugia malayi and the animal parasite Brugia pahangi. Proc Natl Acad Sci USA. 1986, 83: 797-801. (10.1073/pnas.83.3.797) / Proc Natl Acad Sci USA by LA McReynolds (1986)
  16. Blaxter M, Daub J, Guiliano DB, Parkinson J, Whitton C, Project FG: The Brugia malayigenome project: expressed sequence tags and gene discovery. Trans Roy Soc Trop Med Hyg. 2001, / Trans Roy Soc Trop Med Hyg by M Blaxter (2001)
  17. Williams SA, Lizotte-Waniewski MR, Foster J, Guiliano D, Daub J, Scott AL, Slatko B, Blaxter ML: The filarial genome project: analysis of the nuclear, mitochondrial and endosymbiont genomes of Brugia malayi. Int J Parasitol. 2000, 30: 411-419. 10.1016/S0020-7519(00)00014-X. (10.1016/S0020-7519(00)00014-X) / Int J Parasitol by SA Williams (2000)
  18. Meyer BJ: Sex determination and X chromosome dosage compensation. In C. elegans II. Edited by: Riddle DL, Blumenthal T, Meyer BJ, Priess JR. 1997, Plainview, New York: Cold Spring Harbor Laboratory Press, 209-240. / In C. elegans II by BJ Meyer (1997)
  19. Sakaguchi Y, Tada I, Ash LR, Aoki Y: Karyotypes of Brugia pahangi and Brugia malayi (Nematoda: Filaroidea). J Parasitol. 1983, 69: 1090-1093. (10.2307/3280871) / J Parasitol by Y Sakaguchi (1983)
  20. Pastrana DV, Raghavan N, FitzGerald P, Eisinger SW, Metz C, Bucala R, Schleimer RP, Bickel C, Scott AL: Filarial nematode parasites secrete a homologue of the human cytokine macrophage migration inhibitory factor. Infect Immun. 1998, 66: 5955-5963. (10.1128/IAI.66.12.5955-5963.1998) / Infect Immun by DV Pastrana (1998)
  21. Stec I, Wright TJ, van Ommen GJ, de Boer PA, van Haeringen A, Moorman AF, Altherr MR, den Dunnen JT: WHSC1, a 90 kb SET domain-containing gene, expressed in early development and homologous to a Drosophila dysmorphy gene maps in the Wolf-Hirschhorn syndrome critical region and is fused to IgH in t(4;14) multiple myeloma. Hum Mol Genet. 1998, 7: 1071-1082. 10.1093/hmg/7.7.1071. (10.1093/hmg/7.7.1071) / Hum Mol Genet by I Stec (1998)
  22. Stec I, Nagl SB, van Ommen GJ, den Dunnen JT: The PWWP domain: a potential protein-protein interaction domain in nuclear proteins influencing differentiation?. FEBS Lett. 2000, 473: 1-5. 10.1016/S0014-5793(00)01449-6. (10.1016/S0014-5793(00)01449-6) / FEBS Lett by I Stec (2000)
  23. Nishihira J: Macrophage migration inhibitory factor (MIF): its essential role in the immune system and cell growth. J Interferon Cytokine Res. 2000, 20: 751-762. 10.1089/10799900050151012. (10.1089/10799900050151012) / J Interferon Cytokine Res by J Nishihira (2000)
  24. Falcone FH, Loke P, Zang X, MacDonald AS, Maizels RM, Allen JE: A Brugia malayi homolog of macrophage migration inhibitory factor reveals an important link between macrophages and eosinophil recruitment during nematode infection. J Immunol. 2001, 167: 5348-5354. (10.4049/jimmunol.167.9.5348) / J Immunol by FH Falcone (2001)
  25. Marson AL, Tarr DEK, Scott AL: Macrophage migration inhibitory (mif) transcription is significantly elevated in Caenorhabditis elegans dauer larvae. Gene. 2001, 278: 53-62. 10.1016/S0378-1119(01)00706-5. (10.1016/S0378-1119(01)00706-5) / Gene by AL Marson (2001)
  26. Kleemann R, Rorsman H, Rosengren E, Mischke R, Mai NT, Bernhagen J: Dissection of the enzymatic and immunologic functions of macrophage migration inhibitory factor. Full immunologic activity of N-terminally truncated mutants. Eur J Biochem. 2000, 267: 7183-7193. 10.1046/j.1432-1327.2000.01823.x. (10.1046/j.1432-1327.2000.01823.x) / Eur J Biochem by R Kleemann (2000)
  27. Xue Y, Canman JC, Lee CS, Nie Z, Yang D, Moreno GT, Young MK, Salmon ED, Wang W: The human SWI/SNF-B chromatin-remodeling complex is related to yeast rsc and localizes at kinetochores of mitotic chromosomes. Proc Natl Acad Sci USA. 2000, 97: 13015-13020. 10.1073/pnas.240208597. (10.1073/pnas.240208597) / Proc Natl Acad Sci USA by Y Xue (2000)
  28. Nicolas RH, Goodwin GH: Molecular cloning of polybromo, a nuclear protein containing multiple domains including five bromodomains, a truncated HMG-box, and two repeats of a novel domain. Gene. 1996, 175: 233-240. 10.1016/0378-1119(96)82845-9. (10.1016/0378-1119(96)82845-9) / Gene by RH Nicolas (1996)
  29. Altschul SF, Koonin EV: Iterated profile searches with PSI-BLAST-a tool for discovery in protein databases. Trends Biochem Sci. 1998, 23: 444-447. 10.1016/S0968-0004(98)01298-5. (10.1016/S0968-0004(98)01298-5) / Trends Biochem Sci by SF Altschul (1998)
  30. Deiss LP, Feinstein E, Berissi H, Cohen O, Kimchi A: Identification of a novel serine/threonine kinase and a novel 15-kD protein as potential mediators of the gamma interferon-induced cell death. Genes Dev. 1995, 9: 15-30. (10.1101/gad.9.1.15) / Genes Dev by LP Deiss (1995)
  31. Wormpep. [http://www.sanger.ac.uk/Projects/C_elegans/wormpep]
  32. WormBase. [http://www.wormbase.org/]
  33. Friedman R, Hughes AL: Gene duplication and the structure of eukaryotic genomes. Genome Res. 2001, 11: 373-381. 10.1101/gr.155801. (10.1101/gr.155801) / Genome Res by R Friedman (2001)
  34. Lespinet O, Wolf YI, Koonin EV, Aravind L: The role of lineage-specific gene family expansion in the evolution of eukaryotes. Genome Res. 2002, 12: 1048-1059. 10.1101/gr.174302. (10.1101/gr.174302) / Genome Res by O Lespinet (2002)
  35. Blaxter ML: Genes and genomes of Necator americanus and related hookworms. Int J Parasitol. 2000, 30: 347-355. 10.1016/S0020-7519(99)00198-8. (10.1016/S0020-7519(99)00198-8) / Int J Parasitol by ML Blaxter (2000)
  36. Walton AC: Some parasites and their chromosomes. J Parasitol. 1959, 45: 1-20. (10.2307/3274781) / J Parasitol by AC Walton (1959)
  37. Blaxter ML, De Ley P, Garey JR, Liu LX, Scheldeman P, Vierstraete A, Vanfleteren JR, Mackey LY, Dorris M, Frisse LM, et al: A molecular evolutionary framework for the phylum Nematoda. Nature. 1998, 392: 71-75. 10.1038/32160. (10.1038/32160) / Nature by ML Blaxter (1998)
  38. Foster JM, Kamal IH, Daub J, Swan MC, Ingram JR, Ganatra M, Ware J, Guiliano D, Aboobaker A, Moran L, et al: Hybridization to high-density filter arrays of a Brugia malayi BAC library with biotinylated oligonucleotides and PCR products. Biotechniques. 2001, 30: 1216-1218. (10.2144/01306bm06) / Biotechniques by JM Foster (2001)
  39. Parkinson J, Whitton C, Guiliano D, Daub J, Blaxter ML: 200,000 nematode ESTs on the net. Trends Parasitol. 2001, 17: 394-396. 10.1016/S1471-4922(01)01954-7. (10.1016/S1471-4922(01)01954-7) / Trends Parasitol by J Parkinson (2001)
  40. Zang X, Yazdanbakhsh M, Jiang H, Kanost MR, Maizels RM: A novel serpin expressed by blood-borne microfilariae of the parasitic nematode Brugia malayi inhibits human neutrophil serine proteinases. Blood. 1999, 94: 1418-1428. (10.1182/blood.V94.4.1418) / Blood by X Zang (1999)
  41. Maina CV, Grandea AG, Tuyen LTK, Asikin N, Williams SA, McReynolds LA: Dirofilaria immitis: Genomic complexity and characterisation of a structural gene. In Molecular Paradigms for Eradicating Helminthic Parasites. Edited by: MacInnis AJ. 1987, Alan Liss: New York, 193-204. / In Molecular Paradigms for Eradicating Helminthic Parasites by CV Maina (1987)
  42. Reboul J, Vaglio P, Tzellas N, Thierry-Mieg N, Moore T, Jackson C, Shin IT, Kohara Y, Thierry-Mieg D, Thierry-Mieg J, et al: Open-reading-frame sequence tags (OSTs) support the existence of at least 17,300 genes in C. elegans. Nat Genet. 2001, 27: 332-336. 10.1038/85913. (10.1038/85913) / Nat Genet by J Reboul (2001)
  43. Brunner B, Todt T, Lenzner S, Stout K, Schulz U, Ropers HH, Kalscheuer VM: Genomic structure and comparative analysis of nine Fugu genes: conservation of synteny with human chromosome Xp22.2-p22.1. Genome Res. 1999, 9: 437-448. (10.1101/gr.9.5.437) / Genome Res by B Brunner (1999)
  44. Hamer L, Pan H, Adachi K, Orbach MJ, Page A, Ramamurthy L, Woessner JP: Regions of microsynteny in Magnaporthe grisea and Neurospora crassa. Fungal Genet Biol. 2001, 33: 137-143. 10.1006/fgbi.2001.1286. (10.1006/fgbi.2001.1286) / Fungal Genet Biol by L Hamer (2001)
  45. Huynen MA, Snel B, Bork P: Inversions and the dynamics of eukaryotic gene order. Trends Genet. 2001, 17: 304-306. 10.1016/S0168-9525(01)02302-2. (10.1016/S0168-9525(01)02302-2) / Trends Genet by MA Huynen (2001)
  46. Blumenthal T, Steward K: RNA processing and gene structure. In C. elegans II. Edited by: Riddle DL, Blumenthal T, Meyer BJ, Priess JR. 1997, Plainview, New York: Cold Spring Harbor Laboratory Press, 117-146. / In C. elegans II by T Blumenthal (1997)
  47. Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK: A global analysis of Caenorhabditis elegans operons. Nature. 2002, 417: 851-854. 10.1038/nature00831. (10.1038/nature00831) / Nature by T Blumenthal (2002)
  48. Maeda I, Kohara Y, Yamamoto M, Sugimoto A: Large-scale analysis of gene function in Caenorhabditis elegans by high-throughput RNAi. Curr Biol. 2001, 11: 171-176. 10.1016/S0960-9822(01)00052-5. (10.1016/S0960-9822(01)00052-5) / Curr Biol by I Maeda (2001)
  49. Fraser AG, Kamath RS, Zipperlen P, Martinez-Campos M, Sohrmann M, Ahringer J: Functional genomic analysis of C. elegans chromosome I by systematic RNA interference. Nature. 2000, 408: 325-330. 10.1038/35042517. (10.1038/35042517) / Nature by AG Fraser (2000)
  50. Grant D, Cregan P, Shoemaker RC: Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci USA. 2000, 97: 4168-4173. 10.1073/pnas.070430597. (10.1073/pnas.070430597) / Proc Natl Acad Sci USA by D Grant (2000)
  51. Ku HM, Vision T, Liu J, Tanksley SD: Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA. 2000, 97: 9121-9126. 10.1073/pnas.160271297. (10.1073/pnas.160271297) / Proc Natl Acad Sci USA by HM Ku (2000)
  52. Guiliano D, Ganatra M, Ware J, Parrot J, Daub J, Moran L, Brennecke H, Foster JM, Supali T, Blaxter M, et al: Chemiluminescent detection of sequential DNA hybridizations to high- density, filter-arrayed cDNA libraries: a subtraction method for novel gene discovery. Biotechniques. 1999, 27: 146-152. (10.2144/99271rr03) / Biotechniques by D Guiliano (1999)
  53. End sequencing protocol. [http://www.sanger.ac.uk/Teams/Team51/PACBACPrep.shtml]
  54. Organization of the Gap4 manual. [http://www.mrc-lmb.cam.ac.uk/pubseq/manual/gap4_unix_1.html]
  55. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol. 1990, 215: 403-410. 10.1006/jmbi.1990.9999. (10.1016/S0022-2836(05)80360-2) / J Mol Biol by SF Altschul (1990)
  56. 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: 3389-3402. 10.1093/nar/25.17.3389. (10.1093/nar/25.17.3389) / Nucleic Acids Res by SF Altschul (1997)
  57. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B: Artemis: sequence visualization and annotation. Bioinformatics. 2000, 16: 944-945. 10.1093/bioinformatics/16.10.944. (10.1093/bioinformatics/16.10.944) / Bioinformatics by K Rutherford (2000)
  58. Bateman A, Birney E, Durbin R, Eddy SR, Howe KL, Sonnhammer EL: The Pfam protein families database. Nucleic Acids Res. 2000, 28: 263-266. 10.1093/nar/28.1.263. (10.1093/nar/28.1.263) / Nucleic Acids Res by A Bateman (2000)
  59. Nakai K, Kanehisa M: A knowledge base for predicting protein localization sites in eukaryotic cells. Genomics. 1992, 14: 897-911. (10.1016/S0888-7543(05)80111-9) / Genomics by K Nakai (1992)
  60. NemBase. [http://www.nematodes.org/]
  61. Lizotte-Waniewski M, Tawe W, Guiliano DB, Lu W, Liu J, Williams SA, Lustigman S: Identification of potential vaccine and drug target candidates by expressed sequence tag analysis and immunoscreening of Onchocerca volvulus larval cDNA libraries. Infect Immun. 2000, 68: 3491-3501. 10.1128/IAI.68.6.3491-3501.2000. (10.1128/IAI.68.6.3491-3501.2000) / Infect Immun by M Lizotte-Waniewski (2000)
Dates
Type When
Created 22 years, 11 months ago (Sept. 26, 2002, 8:07 a.m.)
Deposited 1 year, 4 months ago (April 25, 2024, 12:06 p.m.)
Indexed 4 months, 3 weeks ago (April 10, 2025, 8:12 a.m.)
Issued 22 years, 11 months ago (Sept. 26, 2002)
Published 22 years, 11 months ago (Sept. 26, 2002)
Published Online 22 years, 11 months ago (Sept. 26, 2002)
Funders 0

None

@article{Guiliano_2002, title={Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes}, volume={3}, ISSN={1474-760X}, url={http://dx.doi.org/10.1186/gb-2002-3-10-research0057}, DOI={10.1186/gb-2002-3-10-research0057}, number={10}, journal={Genome Biology}, publisher={Springer Science and Business Media LLC}, author={Guiliano, DB and Hall, N and Jones, SJM and Clark, LN and Corton, CH and Barrell, BG and Blaxter, ML}, year={2002}, month=sep }