Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Laing, Roz ^a,b   Hunt, Martin ^a   Protasio, Anna V ^a   Saunders, Gary ^b   Mungall, Karen ^c   Laing, Steven ^b   Jackson, Frank ^d   Quail, Michael ^a   Beech, Robin ^e   Berriman, Matthew ^a   Gilleard, John S ^f  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF GLASGOW   (United Kingdom)

^c BRITISH COLUMBIA CANCER AGENCY   (Canada)

^d MOREDUN RESEARCH INSTITUTE   (United Kingdom)

^e MCGILL UNIVERSITY   (Canada)

^f UNIVERSITY OF CALGARY   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; CAENORHABDITIS ELEGANS; CHROMOSOME 1; CONTROLLED STUDY; EXPRESSED SEQUENCE TAG; GENE ORDER; GENE STRUCTURE; GENOME; GENOME ANALYSIS; HAEMONCHUS CONTORTUS; INTRON; NONHUMAN; NUCLEOTIDE SEQUENCE; OPERON; RNA SEQUENCE; SYNTENY; TRANS SPLICING; TRANSCRIPTOMICS; TRANSPOSON; X CHROMOSOME; ANIMAL; CHROMOSOME; CHROMOSOME MAP; COMPARATIVE STUDY; GENE; GENETICS; HAEMONCHUS; METHODOLOGY; MOLECULAR GENETICS; SEQUENCE ANALYSIS;

CAENORHABDITIS ELEGANS; HAEMONCHUS CONTORTUS; NEMATODA; STRONGYLIDA;

HELMINTH RNA; TRANSCRIPTOME;

ANIMALS; CAENORHABDITIS ELEGANS; CHROMOSOME MAPPING; CHROMOSOMES; DNA TRANSPOSABLE ELEMENTS; GENES, HELMINTH; GENOME, HELMINTH; HAEMONCHUS; MOLECULAR SEQUENCE ANNOTATION; RNA, HELMINTH; SEQUENCE ANALYSIS, RNA; SYNTENY; TRANSCRIPTOME; X CHROMOSOME;

EID: 80051674819     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0023216     Document Type: Article

References (46)

1. Couthier A, Smith J, McGarr P, Craig B, Gilleard JS, (2004) Ectopic expression of a Haemonchus contortus GATA transcription factor in Caenorhabditis elegans reveals conserved function in spite of extensive sequence divergence. Mol Biochem Parasitol 133: 241-253.
2. Gilleard JS, (2004) The use of Caenorhabditis elegans in parasitic nematode research. Parasitology 128 (Suppl 1): S49-S70.
3. Knox DP, Redmond DL, Newlands GF, Skuce PJ, Pettit D, et al. (2003) The nature and prospects for gut membrane proteins as vaccine candidates for Haemonchus contortus and other ruminant trichostrongyloids. Int J Parasitol 33: 1129-1137.
4. LeJambre LF, Windon RG, Smith WD, (2008) Vaccination against Haemonchus contortus: performance of native parasite gut membrane glycoproteins in Merino lambs grazing contaminated pasture. Vet Parasitol 153: 302-312.
5. Kaminsky R, Ducray P, Jung M, Clover R, Rufener L, et al. (2008) A new class of anthelmintics effective against drug-resistant nematodes. Nature 452: 176-180.
6. Gilleard JS, (2006) Understanding anthelmintic resistance: the need for genomics and genetics. Int J Parasitol 36: 1227-1239.
7. Prichard R, (2001) Genetic variability following selection of Haemonchus contortus with anthelmintics. Trends Parasitol 17: 445-453.
8. Wolstenholme AJ, Fairweather I, Prichard R, Samson-Himmelstjerna G, Sangster NC, (2004) Drug resistance in veterinary helminths. Trends Parasitol 20: 469-476.
9. Chain PS, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, et al. (2009) Genomics. Genome project standards in a new era of sequencing. Science 326: 236-237.
10. The C. Celegans Sequencing Consortium (1998) Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282: 2012-2018.
11. Duret L, Mouchiroud D, (1999) Expression pattern and, surprisingly, gene length shape codon usage in Caenorhabditis, Drosophila, and Arabidopsis. Proc Natl Acad Sci U S A 96: 4482-4487.
12. Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, et al. (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biol 1: E45.
13. Deutsch M, Long M, (1999) Intron-exon structures of eukaryotic model organisms. Nucleic Acids Res 27: 3219-3228.
14. Spieth J, Lawson D, (2006) Overview of gene structure. WormBook pp. 1-10.
15. Redman E, Grillo V, Saunders G, Packard E, Jackson F, et al. (2008) Genetics of mating and sex determination in the parasitic nematode Haemonchus contortus. Genetics 180: 1877-1887.
16. Rufener L, Maser P, Roditi I, Kaminsky R, (2009) Haemonchus contortus acetylcholine receptors of the DEG-3 subfamily and their role in sensitivity to monepantel. PLoS Pathog 5: e1000380.
17. Redmond DL, Knox DP, (2001) Haemonchus contortus SL2 trans-spliced RNA leader sequence. Mol Biochem Parasitol 117: 107-110.
18. Laughton DL, Amar M, Thomas P, Towner P, Harris P, et al. (1994) Cloning of a putative inhibitory amino acid receptor subunit from the parasitic nematode Haemonchus contortus. Receptors Channels 2: 155-163.
19. Callaghan MJ, Beh KJ, (1994) Characterization of a tandemly repetitive DNA sequence from Haemonchus contortus. Int J Parasitol 24: 137-141.
20. Grillo V, Jackson F, Gilleard JS, (2006) Characterisation of Teladorsagia circumcincta microsatellites and their development as population genetic markers. Mol Biochem Parasitol 148: 181-189.
21. Hoekstra R, Criado-Fornelio A, Fakkeldij J, Bergman J, Roos MH, (1997) Microsatellites of the parasitic nematode Haemonchus contortus: polymorphism and linkage with a direct repeat. Mol Biochem Parasitol 89: 97-107.
22. Vanfleteren JR, Van de PY, Blaxter ML, Tweedie SA, Trotman C, et al. (1994) Molecular genealogy of some nematode taxa as based on cytochrome c and globin amino acid sequences. Mol Phylogenet Evol 3: 92-101.
23. Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, et al. (2004) A transcriptomic analysis of the phylum Nematoda. Nat Genet 36: 1259-1267.
24. Coghlan A, Wolfe KH, (2002) Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12: 857-867.
25. Ghedin E, Wang S, Spiro D, Caler E, Zhao Q, et al. (2007) Draft genome of the filarial nematode parasite Brugia malayi. Science 317: 1756-1760.
26. Guiliano DB, Hall N, Jones SJ, Clark LN, Corton CH, et al. (2002) Conservation of long-range synteny and microsynteny between the genomes of two distantly related nematodes. Genome Biol 3: RESEARCH0057.
27. Hillier LW, Miller RD, Baird SE, Chinwalla A, Fulton LA, et al. (2007) Comparison of C. elegans and C. briggsae genome sequences reveals extensive conservation of chromosome organization and synteny. PLoS Biol 5: e167.
28. Ranz JM, Casals F, Ruiz A, (2001) How malleable is the eukaryotic genome? Extreme rate of chromosomal rearrangement in the genus Drosophila. Genome Res 11: 230-239.
29. Blumenthal T, Gleason KS, (2003) Caenorhabditis elegans operons: form and function. Nat Rev Genet 4: 112-120.
30. Qian W, Zhang J, (2008) Evolutionary dynamics of nematode operons: easy come, slow go. Genome Res 18: 412-421.
31. Graber JH, Salisbury J, Hutchins LN, Blumenthal T, (2007) C. elegans sequences that control trans-splicing and operon pre-mRNA processing. RNA 13: 1409-1426.
32. Liu C, Oliveira A, Chauhan C, Ghedin E, Unnasch TR, (2010) Functional analysis of putative operons in Brugia malayi. Int J Parasitol 40: 63-71.
33. Bessereau JL, (2006) Transposons in C. elegans. WormBook pp. 1-13.
34. Caceres M, Ranz JM, Barbadilla A, Long M, Ruiz A, (1999) Generation of a widespread Drosophila inversion by a transposable element. Science 285: 415-418.
35. Duret L, Marais G, Biemont C, (2000) Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics 156: 1661-1669.
36. Coghlan A, Wolfe KH, (2002) Fourfold faster rate of genome rearrangement in nematodes than in Drosophila. Genome Res 12: 857-867.
37. Chen S, Li X, (2007) Transposable elements are enriched within or in close proximity to xenobiotic-metabolizing cytochrome P450 genes. BMC Evol Biol 7: 46.
38. Tanizawa Y, Kuhara A, Inada H, Kodama E, Mizuno T, et al. (2006) Inositol monophosphatase regulates localization of synaptic components and behavior in the mature nervous system of C. elegans. Genes Dev 20: 3296-3310.
39. Leroy S, Duperray C, Morand S, (2003) Flow cytometry for parasite nematode genome size measurement. Mol Biochem Parasitol 128: 91-93.
40. Jackson F, Hoste H, (2010) In vitro screening of plant resources for extra-nutritional attributes in ruminants: nuclear and related methodologies. In: Vercoe PE, Makkar HPS, Schlink AC, editors. In Vitro Methods for the Primary Screening of Plant Products for Direct Activity against Ruminant Gastrointestinal Nematodes Springer Netherlands pp. 25-45.
41. Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760.
42. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, et al. (2009) The Sequence Alignment/Map format and SAMtools. Bioinformatics 25: 2078-2079.
43. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, et al. (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945.
44. Carver T, Bohme U, Otto TD, Parkhill J, Berriman M, (2010) BamView: viewing mapped read alignment data in the context of the reference sequence. Bioinformatics 26: 676-677.
45. Carver TJ, Rutherford KM, Berriman M, Rajandream MA, Barrell BG, et al. (2005) ACT: the Artemis Comparison Tool. Bioinformatics 21: 3422-3423.
46. Abbott JC, Aanensen DM, Rutherford K, Butcher S, Spratt BG, (2005) WebACT- an online companion for the Artemis Comparison Tool. Bioinformatics 21: 3665-3666.