Limited microsynteny between the genomes of Pristionchus pacificus and Caenorhabditis elegans

Nucleic Acids Research

Volumn 31, Issue 10, 2003, Pages 2553-2560

  Lee, Kwang Zin ^a   Eizinger, Andreas ^a,b   Nandakumar, Ramkumar ^a   Schuster, Stephan C ^a   Sommer, Ralf J ^a  

^a MAX PLANCK INSTITUTE FOR DEVELOPMENTAL BIOLOGY   (Germany)

^b STANFORD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN PAL 1; UNCLASSIFIED DRUG; COMPLEMENTARY DNA; HELMINTH DNA;

ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME 3; CHROMOSOME REARRANGEMENT; CONTROLLED STUDY; DNA FLANKING REGION; GENE IDENTIFICATION; GENE LOCATION; GENE SEQUENCE; MOLECULAR EVOLUTION; NEMATODE; NONHUMAN; NUCLEOTIDE SEQUENCE; OPEN READING FRAME; ORTHOLOGY; PRIORITY JOURNAL; PRISTIONCHUS PACIFICUS; SYNTENY; AMINO ACID SEQUENCE; ANIMAL; CHEMISTRY; CHROMOSOME MAP; DNA SEQUENCE; GENE; GENETICS; GENOME; MOLECULAR CLONING; MOLECULAR GENETICS; SEQUENCE HOMOLOGY; SPECIES DIFFERENCE;

CAENORHABDITIS; CAENORHABDITIS ELEGANS; INVERTEBRATA; NEMATODA; PRISTIONCHUS; PRISTIONCHUS PACIFICUS;

AMINO ACID SEQUENCE; ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; CLONING, MOLECULAR; DNA, COMPLEMENTARY; DNA, HELMINTH; GENES, HELMINTH; GENOME; MOLECULAR SEQUENCE DATA; NEMATODA; SEQUENCE ANALYSIS, DNA; SEQUENCE HOMOLOGY, AMINO ACID; SPECIES SPECIFICITY; SYNTENY;

EID: 0038043324     PISSN: 03051048     EISSN: None     Source Type: Journal    
DOI: 10.1093/nar/gkg359     Document Type: Article

References (33)

1. Sommer,R.J. (2001) As good as they get: cells in nematode vulva development and evolution. Curr. Opin. Cell Biol., 13, 715-720.
2. Eizinger,A., Jungblut,B. and Sommer,R.J. (1999) Evolutionary change in the functional specificity of genes. Trends Genet., 15, 197-202.
3. Simpson,P. (2002) Evolution of development in closely related species of flies and worms. Nature Rev. Genet., 3, 907-991.
4. Sommer,R.J. (2000) Evolution of nematode development. Curr. Opin. Genet. Dev., 10, 443-448.
5. Wang,M. and Sternberg,P.W. (2001) Pattern formation during C. elegans vulval induction. Curr. Topics Dev. Biol., 51, 189-220.
6. Eizinger,A. and Sommer,R.J. (1997) The homeotic gene lin-39 and the evolution of nematode epidermal cell fates. Science, 278, 452-455.
7. Sommer,R.J., Eizinger,A., Lee,K.Z., Jungblut,B., Bubeck,A. and Schlak,I. (1998) The Pristionchus HOX gene Ppa-lin-39 inhibits programmed cell death to specify the vulva equivalence group and is not required during vulval induction. Development, 125, 3865-3873.
8. Jungblut,B. and Sommer,R.J. (1998) The Pristionchus pacificus mab-5 gene is involved in the regulation of ventral epidermal cell fates. Curr. Biol., 8, 775-778.
9. Jungblut,B. and Sommer,R.J. (2001) The nematode even-skipped homolog vab-7 regulates gonad and vulva position in Pristionchus pacificus. Development, 128, 253-261.
10. Srinivasan,J., Pires-daSilva,A., Gutierrez,A., Zheng,M., Jungblut,B., Witte,H., Schlak,I, and Sommer,R.J. (2001) Microevolutionary analysis of the nematode genus Pristionchus suggests a recent evolution of redundant developmental mechanisms during vulva formation. Evol. Dev., 3, 229-240.
11. Schlak,I., Eizinger,A. and Sommer,R.J. (1997) High rate of restriction fragment length polymorphisms between two populations of the nematode Pristionchus pacificus (Diplogastridae). J. Zool. Syst. Evol., 35, 137-142.
12. Srinivasan,J., Sinz,W., Lanz,C., Brand,A., Nandakumar,R., Raddatz,G., Witte,H., Keller,H., Kipping,I., Pires-DaSilva,A. et al. (2002) A bacterial artificial chromosome-based genetic linkage map of the nematode Pristionchus pacificus. Genetics, 162, 129-134.
13. McCarter,J.P., Clifton,S.W., Bird,D.M. and Waterston,R.H. (2002) Nematode gene sequences, update for June 2002. J. Nematol., 34, 71-74.
14. Kent,W.J. and Zahler,A.M. (2000) Conservation, regulation, synteny, and introns in a large-scale C. briggsae-C. elegans genomic alignment. Genome Res., 10, 1115-1125.
15. Guiliano,D.B., Hall,N., Jones,S.J., Clark,L.N., Corton,C.H., Barrell,B.G. and Blaxter,M.L. (2002) Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol., 3, 57.1-57.14.
16. Ranasinghe,C. and Hobbs,A.A. (1998) Isolation and characterization of two cytochrome P450 cDNA clones for CYP6B6 and CYP6B7 from Helicoverpa armigera (Hubner): possible involvement of CYP6B7 in pyrethroid resistance. Insect Biochem. Mol. Biol., 28, 571-580.
17. Frohman,M.A. (1994) On beyond classic RACE (rapid amplification of cDNA ends). PCR Methods Appl., 4, S40-S58.
18. Hunter,C.P. and Kenyon,C. (1996) Spatial and temporal controls target pal-1 blastomere-specification activity to a single blastomere lineage in C. elegans embryos. Cell, 87, 217-226.
19. Waring,D.A. and Kenyon,C. (1990) Selective silencing of cell communication influences anteroposterior pattern formation in C. elegans. Cell, 60, 123-131.
20. Waring,D.A. and Kenyon,C. (1991) Regulation of cellular responsiveness to inductive signals in the developing C. elegans nervous system. Nature, 350, 712-715.
21. Fleischmann,R.D., Adams,M.D., White,O., Clayton,R.A., Kirkness,E.F., Kerlavage,A.R., Bult,C.J., Tomb,J.F., Dougherty,B.A., Merrick,J.M. et al. (1995) Whole-genome random sequencing and assembly of Haemophilus influenzae Rd. Science, 269, 496-512.
22. Ewing,B. and Green,P. (1998) Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res., 8, 186-194.
23. Brosch,R., Gordon,S.V., Billault,A., Garnier,T., Eiglmeier,K., Soravito,C., Barrell,B.G. and Cole,S.T. (1998) Use of a Mycobacterium tuberculosis H37Rv bacterial artificial chromosome library for genome mapping, sequencing and comparative genomics. Infect. Immun., 66, 2221-2229.
24. Harris,T.W., Lee,R., Schwarz,E., Bradnam,K., Lawson,D., Chen,W., Blasier,D., Kenny,E., Cunningham,F., Kishore,R. et al. (2003) WormBase: a cross-species database for comparative genomics. Nucleic Acids Res., 31, 133-137.
25. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
26. Waterston,R.H., Lander,E.S. and Sulston,J.E. (2002) On the sequencing of the human genome. Proc. Natl Acad. Sci. USA, 99, 3712-3716.
27. Venter,J.C., Adams,M.D., Myers,E.W., Li,P.W., Mural,R.J., Sutton,G.G., Smith,H.O., Yandell,M., Evans,C.A., Holt,R.A. et al. (2001) The sequence of the human genome. Science, 291, 1304-1351.
28. Adams,M.D., Celniker,S.E., Holt,R.A., Evans,C.A., Gocayne,J.D., Amanatides,P.G., Scherer,S.E., Li,P.W., Hoskins,R.A., Galle,R.F. et al. (2000) The genome sequence of Drosophila melanogaster. Science, 287, 2185-2195.
29. The C. elegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science, 282, 2012-2018.
30. Sommer,R.J., Carta,L.K., Kim,S.-y. and Sternberg,P.W. (1996) Morphological, genetic and molecular description of Pristionchus pacificus sp. n. (Nematoda: Neodiplogastridae). Fundam. Appl. Nematol., 19, 511-521.
31. Aparicio,S., Chapman,J., Stupka,E., Putnam,N., Chia,J.M., Dehal,P., Christoffels,A., Rash,S., Hoon,S., Smit,A. et al. (2002) Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science, 297, 1301-1310.
32. Coghlan,A. and Wolfe,K.H. (2002) Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res., 12, 857-867.
33. Grandien,K. and Sommer,R.J. (2001) Functional comparison of the nematode Hox gene lin-39 in C. elegans and P. pacificus reveals evolutionary conservation of protein function despite divergence of primary sequences. Genes Dev., 15, 2161-2172.