Skip to main content
SpringerLink
Log in

Exploring the transcriptome of the burrowing nematode Radopholus similis

  • Original Paper
  • Published:
Molecular Genetics and Genomics Aims and scope Submit manuscript

Abstract

Radopholus similis is an important nematode pest on fruit crops in the tropics. Unraveling the transcriptome of this migratory plant-parasitic nematode can provide insight in the parasitism process and lead to more efficient control measures. For the first high throughput molecular characterization of this devastating nematode, 5,853 expressed sequence tags from a mixed stage population were generated. Adding 1,154 tags from the EST division of GenBank for subsequent analysis, resulted in a total of 7,007 ESTs, which represent approximately 3,200 genes. The mean G + C content of the nucleotides at the third codon position (GC3%) was calculated to be as high as 64.8%, the highest for nematodes reported to date. BLAST-searches resulted in about 70% of the clustered ESTs having homology to (DNA and protein) sequences from the GenBank database, whereas one-third of them did not match to any known sequence. Roughly 40% of these latter sequences are predicted to be coding, representing putative novel protein coding genes. Functional annotation of the sequences by GO annotation revealed the abundance of genes involved in reproduction and development, which reflects the nematode population biology. Genes with a role in the parasitism process are identified, as well as genes essential for nematode survival, providing information useful for parasite control. No evidence was found for the presence of trans-spliced leader sequences commonly occurring in nematodes, despite the use of various approaches. In conclusion, we found three different sources for the EST sequences: the majority has a nuclear origin, approximately 1% of the EST sequences are derived from the mitochondrial transcriptome, and interestingly, 1% of the tags are with high probability derived from Wolbachia, providing the first molecular indication for the presence of this endosymbiont in a plant-parasitic nematode.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Abbreviations

cDNA:

Complementary DNA

EST:

Expressed sequence tag

ORF:

Open reading frame

GO:

Gene ontology

mRNA:

Messenger RNA

aa:

Amino acid

PPN:

Plant-parasitic nematode

APN:

Animal-parasitic nematode

FLN:

Free-living nematode

References

  • Aaronson JS, Eckman B, Blevins RA, Borkowski JA, Myerson J, Imran S, Elliston KO (1996) Toward the development of a gene index to the human genome: an assessment of the nature of high-throughput EST sequence data. Genome Res 6:829–845

    Article  PubMed  CAS  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Atkinson H, Grimwood S, Johnston K, Green J (2004) Prototype demonstration of transgenic resistance to the nematode Radopholus similis conferred on banana by a cystatin. Transgenic Res 13:135–142

    Article  PubMed  CAS  Google Scholar 

  • Bakhetia M, Charlton WL, Urwin PE, McPherson MJ, Atkinson HJ (2005) RNA interference and plant parasitic nematodes. Trends Plant Sci 10:362–367

    Article  PubMed  CAS  Google Scholar 

  • Basak S, Ghosh TC (2005) On the origin of genomic adaptation at high temperature for prokaryotic organisms. Biochem Biophys Res Commun 330:629–632

    Article  PubMed  CAS  Google Scholar 

  • Belle EM, Smith N, Eyre-Walker A (2002) Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol 55:256–363

    Article  Google Scholar 

  • Bentwich I, Avniel A, Karov Y, Aharonov R, Gilad S, Barad O, Barzilai A, Einat P, Einav U, Meiri E, Sharon E, Spector Y, Bentwich Z (2005) Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet 37:766–770

    Article  PubMed  CAS  Google Scholar 

  • Berriman M, Aslett M, Hall N, Ivens A (2001) Parasites are GO. Trends Parasitol 17:463–464

    Article  PubMed  CAS  Google Scholar 

  • Blumenthal T, Evans D, Link CD, Guffanti A, Lawson D, Thierry-Mieg J, Thierry-Mieg D, Chiu WL, Duke K, Kiraly M, Kim SK (2002) A global analysis of Caenorhabditis elegans operons. Nature 417:851–854

    Article  PubMed  CAS  Google Scholar 

  • Boguski MS, Lowe TMJ, Tolstoshev CM (1993) dbEST - database for “expressed sequence tags”. Nat Genet 4:332–333

    Article  PubMed  CAS  Google Scholar 

  • Chen W-H, Wang X-X, Lin W, He X-W, Wu Z-Q, Lin Y, Hu S-N, Wang X-N (2006) Analysis of 10,000 ESTs from lymphocytes of the cynomolgus monkey to improve our understanding of its immune system. BMC Genomics 7:82. doi:10.1186/1471-2164-7-82

    Article  PubMed  Google Scholar 

  • Conesa A, Gotz S, Garcia-Gomez JM, Terol J, Talon M, Robles M (2005) Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21:3674–3676

    Article  PubMed  CAS  Google Scholar 

  • Cutter AD, Wasmuth JD, Blaxter ML (2006) The evolution of biased codon and amino acid usage in nematode genomes. Mol Biol Evol 23:2303–2315

    Article  PubMed  CAS  Google Scholar 

  • Dubreuil G, Magliano M, Deleury E, Abad P, Rosso MN (2007) Transcriptome analysis of root-knot nematode functions induced in the early stages of parasitism. New Phytol 176:426–436

    Article  PubMed  CAS  Google Scholar 

  • Elsen A, Jain SM, Swennen R, De Waele D (2004) Recent developments in early in vitro screening for resistance against migratory endoparasitic nematodes in Musa. Banana improvement: cellular, molecular biology, and induced mutations. Proceedings of a meeting held in Leuven, Belgium, 24–28 September 2001, Science publishers, Inc

  • Emanuelsson O, Brunak S, von Heijne G, Nielsen H (2007) Locating proteins in the cell using TargetP, SignalP, and related tools. Nat Protoc 2:953–971

    Article  PubMed  CAS  Google Scholar 

  • Foster J, Ganatra M, Kama I, Ware J, Makarova K, Ivanova N, Bhattacharyya A, Kapatral V, Kumar S, Posfai J, Vincze T, Ingram J, Moran L, Lapidus A, Omelchenko M, Kyrpides N, Ghedin E, Wang S, Goltsman E, Joukov V, Ostrovskaya O, Tsukerman K, Mazur M, Comb D, Koonin E, Slatko B (2005) The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode. PLOS Biol 3:0599–0614

    Article  CAS  Google Scholar 

  • Garofalo A, Kennedy MW, Bradley JE (2003) The FAR proteins of parasitic nematodes: their possible involvement in the pathogenesis of infection and the use of Caenorhabditis elegans as a model system to evaluate their function. Med Microbiol Immunol 192:47–52

    PubMed  CAS  Google Scholar 

  • Gheysen G, Vanholme B (2007) RNAi from plants to nematodes. Trends Biotechnol 25:89–92

    Article  PubMed  CAS  Google Scholar 

  • Gissi C, Pesole G (2003) Transcript mapping and genome annotation of Ascidian mtDNA using EST data. Genome Res 13:2203–2212

    Article  PubMed  CAS  Google Scholar 

  • Guiliano DB, Blaxter ML (2006) Operon conservation and the evolution of trans-splicing in the phylum Nematoda. PLoS Genet 2:e198. doi:10.1371/journal.pgen.0020198

    Article  PubMed  Google Scholar 

  • Haegeman A, Jacob J, Vanholme B, Kyndt T, Gheysen G (2008) A family of GHF5 endo-1,4-beta-glucanases in the migratory plant-parasitic nematode Radopholus similis. Plant Pathol (in press). doi:10.1111/j.1365-3059.2007.01814.x

  • Hammond MP, Bianco AE (1992) Genes and genomes of parasitic nematodes. Parasitol Today 8:299–305

    Article  PubMed  CAS  Google Scholar 

  • He Y, Jones J, Armstrong M, Lamberti F, Moens M (2005) The mitochondrial genome of Xiphinema americanum sensu stricto (Nematoda: Enoplea): considerable economization in the length and structural features of encoded genes. J Mol Evol 61:819–833

    Article  PubMed  CAS  Google Scholar 

  • Hirokawa T, Boon-Chieng S, Mitaku S (1998) SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics 14:378–379

    Article  PubMed  CAS  Google Scholar 

  • Hise AG, Gillette-Ferguson I, Pearlman E (2004) The role of endosymbiotic Wolbachia bacteria in filarial disease. Cell Microbiol 6:97–104

    Article  PubMed  CAS  Google Scholar 

  • Hotopp JCD, Clark ME, Oliveira DCSG, Foster JM, Fischer P, Torres MCM, Giebel JD, Kumar N, Ishmael N, Wang S, Ingram J, Nene RV, Shepard J, Tomkins J, Richards S, Spiro DJ, Ghedin E, Slatko BE, Tettelin H, Werren JH (2007) Widespread lateral gene transfer from intracellular bacteria to multicellular eukaryotes. Science 317:1753–1756

    Article  PubMed  CAS  Google Scholar 

  • Huang X, Madan A (1999) CAP3: a DNA sequence assembly program. Genome Res 9:868–877

    Article  PubMed  CAS  Google Scholar 

  • Iseli C, Jongeneel V, Bucher P (1999) ESTScan: a program for detecting, evaluating, and reconstructing potential coding regions in EST sequences. Proc Int Conf Intell Syst Mol Biol 138–148

  • Jabbari K, Bernardi G (2004) Body temperature and evolutionary genomics of vertebrates: a lesson from the genomes of Takifugu rubripes and Tetraodon nigroviridis. Gene 333:179–181

    Article  PubMed  CAS  Google Scholar 

  • Jacob J, Vanholme B, Haegeman A, Gheysen G (2007) Four transthyretin-like genes of the migratory plant-parasitic nematode Radopholus similis: members of an extensive nematode-specific family. Gene 402:9–19

    Article  PubMed  CAS  Google Scholar 

  • Jones JT, Reavy B, Smant G, Prior AE (2004) Glutathione peroxidases of the potato cyst nematode Globodera rostochiensis. Gene 324:47–54

    Article  PubMed  CAS  Google Scholar 

  • Kamath RS, Fraser AG, Dong Y, Poulin G, Durbin R, Gotta M, Kanapin A, Le Bot N, Moreno S, Sohrmann M, Welchman DP, Zipperlen P, Ahringer J (2003) Systematic functional analysis of the Caenorhabditis elegans genome using RNAi. Nature 421:231–237

    Article  PubMed  CAS  Google Scholar 

  • Kennedy MW, Allen JE, Wright AS, McCruden AB, Cooper A (1995) The gp15/400 polyprotein antigen of Brugia malayi binds fatty acids and retinoids. Mol Biochem Parasitol 71:41–50

    Article  PubMed  CAS  Google Scholar 

  • Kikuchi T, Aikawa T, Kosaka H, Pritchard L, Ogura N, Jones JT (2007) Expressed sequence tag (EST) analysis of the pine wood nematode Bursaphelenchus xylophilus and B. mucronatus. Mol Biochem Parasitol 115:9–17

    Article  Google Scholar 

  • Kramer L, Passeri B, Corona S, Simoncini L, Casiraghi M (2003) Immunohistochemical/immunogold detection and distribution of the endosymbiont Wolbachia of Dirofilaria immitis and Brugia pahangi using a polyclonal antiserum raised against WSP (Wolbachia surface protein). Parasitol Res 89:381–386

    Article  PubMed  CAS  Google Scholar 

  • Ledger TN, Jaubert S, Bosselut N, Abad P, Rosso M-N (2006) Characterization of a new beta-1,4-endoglucanase gene from the root-knot nematode Meloidogyne incognita and evolutionary scheme for phytonematode family 5 glycosyl hydrolases. Gene 382:121–128

    Article  PubMed  CAS  Google Scholar 

  • Leroy S, Bouamer S, Morand S, Fargette M (2007) Genome size of plant-parasitic nematodes. Nematology 9:449–450

    Article  Google Scholar 

  • Lim LP, Lau NC, Garrett-Engele P, Grimson A, Schelter JM, Castle J, Bartel DP, Linsley PS, Johnson JM (2005) Microarray analysis shows that some microRNAs downregulate large numbers of target mRNAs. Nature 433:769–773

    Article  PubMed  CAS  Google Scholar 

  • Liu D, Graber J (2006) Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. BMC Bioinformatics 7:77. doi:10.1186/1471-2105-7-77

    Article  PubMed  CAS  Google Scholar 

  • Liu F, Lu J, Hu W, Wang SY, Cui SJ, Chi M, Yan Q, Wang XR, Song HD, Xu XN, Wang JJ, Zhang XL, Zhang X, Wang ZQ, Xue CL, Brindley PJ, McManus DP, Yang PY, Feng Z, Chen Z, Han ZG (2006) New perspectives on host-parasite interplay by comparative transcriptomic and proteomic analyses of Schistosoma japonicum. PLoS Pathog 2:e29. doi:10.1371/journal.ppat.0020029

    Article  PubMed  Google Scholar 

  • Mao X, Cai T, Olyarchuk JG, Wei L (2005) Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary. Bioinformatics 21:3787–3793

    Article  PubMed  CAS  Google Scholar 

  • McCarter JP, Mitreva MD, Martin J, Dante M, Wylie T, Rao U, Pape D, Bowers Y, Theising B, Murphy CV, Kloek AP, Chiapelli BJ, Clifton SW, Bird DM, Waterston RH (2003) Analysis and functional classification of transcripts from the nematode Meloidogyne incognita. Genome Biol 4:R26. doi:10.1186/gb-2003-4-4-r26

    Article  PubMed  Google Scholar 

  • Mitreva M, Elling AA, Dante M, Kloek AP, Kalyanaraman A, Aluru S, Clifton SW, Bird DM, Baum TJ, McCarter JP (2004) A survey of SL1-spliced transcipts from the root-lesion nematode Pratylenchus penetrans. Mol Genet Genomics 272:138–148

    Article  PubMed  CAS  Google Scholar 

  • Mitreva M, Wendl MC, Martin J, Wylie T, Yin Y, Larson A, Parkinson J, Waterston RH, McCarter JP (2006) Codon usage patterns in Nematoda: analysis based on over 25 million codons in thirty-two species. Genome Biol 7:R75. doi:10.1186/gb-2006-7-8-r75

    Article  PubMed  Google Scholar 

  • Munoz E, Bogarad L, Deem M (2004) Microarray and EST database estimates of mRNA expression levels differ: the protein length versus expression curve for C. elegans. BMC Genomics 5:30–30

    Article  PubMed  Google Scholar 

  • Nagaraj SH, Deshpande N, Gasser RB, Ranganathan S (2007a) ESTExplorer: an expressed sequence tag (EST) assembly and annotation platform. Nucleic Acids Res 35:W143–W147. doi:10.1093/nar/gkm378

    Article  PubMed  Google Scholar 

  • Nagaraj SH, Gasser RB, Ranganathan S (2007b) A hitchhiker’s guide to expressed sequence tag (EST) analysis. Brief Bioinform 8:6–21

    Article  PubMed  CAS  Google Scholar 

  • Nishikawa T, Nagai K (1996) EST error analysis in a large-scale GenBank search of ESTs using rapid-identity searching program for DNA sequences. In: Genome mapping and sequencing, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New York

  • Noel GR, Atibalentja N (2006) “Candidatus Paenicardinium endonii”, an endosymbiont of the plant-parasitic nematode Heterodera glycines (Nemata: Tylenchida), affiliated to the phylum Bacteroidetes. Int J Syst Evol Microbiol 56:1697–1702

    Article  PubMed  CAS  Google Scholar 

  • O’Bannon JH (1977) Worldwide dissemination of Radopholus similis and its importance in crop production. J Nematol 9:16–25

    Google Scholar 

  • Opperman CH, Bird DM (1998) The soybean cyst nematode, Heterodera glycines: a genetic model system for the study of plant-parasitic nematodes. Current Opin Plant Biol 1:342–346

    Article  CAS  Google Scholar 

  • Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J (2003) TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets. Bioinformatics 19:651–652

    Article  PubMed  CAS  Google Scholar 

  • Price NS (2006) The banana burrowing nematode, Radopholus similis (Cobb) Thorne, in the lake Victoria region of East Africa: its introduction, spread and impact. Nematology 8:801–817

    Article  Google Scholar 

  • Prior A, Jones JT, Blok VC, Beauchamp J, McDermott L, Cooper A, Kennedy MW (2001) A surface-associated retinol- and fatty acid-binding protein (Gp-FAR-1) from the potato cyst nematode Globodera pallida: lipid binding activities, structural analysis and expression pattern. Biochem J 356:387–394

    Article  PubMed  CAS  Google Scholar 

  • Ranganathan S, Nagaraj SH, Hu M, Strube C, Schnieder T, Gasser RB (2007) A transcriptomic analysis of the adult stage of the bovine lungworm, Dityocaulus viviparus. BMC Genomics 8:311. doi:10.1186/1471-2164-8-311

    Article  PubMed  Google Scholar 

  • Richly E, Leister D (2004) NUMTs in sequenced eukaryotic genomes. Mol Biol Evol 21:1081–1084

    Article  PubMed  CAS  Google Scholar 

  • Robertson L, Robertson WM, Sobczak M, Helder J, Tetaud E, Ariyanayagam MR, Ferguson MAJ, Fairlamb A, Jones JT (2000) Cloning, expression and functional characterisation of a peroxiredoxin from the potato cyst nematode Globodera rostochiensis. Mol Biochem Parasitol 111:41–49

    Article  PubMed  CAS  Google Scholar 

  • Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP (2006) Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell 127:1193–1207

    Article  PubMed  CAS  Google Scholar 

  • Sarah JL, Pinochet J, Stanton J (1996) The burrowing nematode of bananas, Radopholus similis Cobb, 1913. International network for the improvement of banana and plantain, Montpellier, France

  • Schiex T, Gouzy J, Moisan A, de Oliveira Y (2003) FrameD: a flexible program for quality check and gene prediction in prokaryotic genomes and noisy matured eukaryotic sequences. Nucleic Acids Res 31:3738–3741

    Article  PubMed  CAS  Google Scholar 

  • Schwarz EM, Antoshechkin I, Bastiani C, Bieri T, Blasiar D, Canaran P, Chan J, Chen N, Chen WJ, Davis P, Fiedler TJ, Girard L, Harris TW, Kenny EE, Kishore R, Lawson D, Lee R, Muller HM, Nakamura C, Ozersky P, Petcherski A, Rogers A, Spooner W, Tuli MA, Van Auken K, Wang D, Durbin R, Spieth J, Stein LD, Sternberg PW (2006) WormBase: better software, richer content. Nucleic Acids Res 34:D475–D478

    Article  PubMed  CAS  Google Scholar 

  • Smant G, Stokkermans JPWG, Yan YT, de Boer JM, Baum TJ, Wang XH, Hussey RS, Gommers FJ, Henrissat B, Davis EL, Helder J, Schots A, Bakker J (1998) Endogenous cellulases in animals: isolation of beta-1,4-endoglucanase genes from two species of plant-parasitic cyst nematodes. PNAS 95:4906–4911

    Article  PubMed  CAS  Google Scholar 

  • Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D’Eustachio P, Fitch DHA, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH (2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLOS Biol 1:e45–e45

    Article  PubMed  Google Scholar 

  • Stoffelen R, Verlinden R, Pinochet J, Swennen RL, De Waele D (2000) Host plant response of Fusarium wilt resistant Musa genotypes to Radopholus similis and Pratylenchus coffeae. Int J Pest Manag 46:289–293

    Article  Google Scholar 

  • Taylor MJ, Bilo K, Cross HF, Archer JP, Underwood AP (1999) 16S rDNA phylogeny and ultrastructural characterization of Wolbachia intracellular bacteria of the filarial nematodes Brugia malayi, B. pahangi, and Wuchereria bancrofti. Exp Parasitol 91:356–361

    Article  PubMed  CAS  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    Article  PubMed  CAS  Google Scholar 

  • Tytgat T, Vercauteren I, Vanholme B, De Meutter J, Vanhoutte I, Gheysen G, Borgonie G, Coomans A, Gheysen G (2005) An SXP/RAL-2 protein produced by the subventral pharyngeal glands in the plant parasitic root-knot nematode Meloidogyne incognita. Parasitol Res 95:50–54

    Article  PubMed  Google Scholar 

  • United Nations Environment Programme (1995) Report of the methyl bromide technical options committee. Montreal protocol on substances that deplete the ozone layer

  • Vandekerckhove TTM, Coomans A, Cornelis K, Baert P, Gillis M (2002) Use of the Verrucomicrobia-specific probe EUB338-III and fluorescent in situ hybridization for detection of “Candidatus Xiphinematobacter” cells in nematode hosts. Appl Environ Microbiol 68:3121–3125

    Article  PubMed  CAS  Google Scholar 

  • Wang J-PZ, Lindsay BG, Cui L, Wall PK, Marion J, Zhang J, dePamphilis CW (2006a) Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics 6:300

    Article  Google Scholar 

  • Wang HC, Susko E, Roger AJ (2006b) On the correlation between genomic G + C content and optimal growth temperature in prokaryotes: data quality and confounding factors. Biochem Biophys Res Commun 342:681–684

    Article  PubMed  CAS  Google Scholar 

  • Washietl S, Hofacker IL, Stadler PF (2005) Fast and reliable prediction of noncoding RNAs. PNAS 102:2454–2459

    Article  PubMed  CAS  Google Scholar 

  • Wasmuth JD, Blaxter ML (2004) Prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5:187

    Article  PubMed  Google Scholar 

  • Wuyts N, Lognay G, Verscheure M, Marlier M, De Waele D, Swennen R (2007) Potential physical and chemical barriers to infection by the burrowing nematode Radopholus similis in roots of susceptible and resistant banana (Musa spp.). Plant Pathol 56:878–890

    Article  CAS  Google Scholar 

  • Wylie T, Martin JC, Dante M, Mitreva MD, Clifton SW, Chinwalla A, Waterston RH, Wilson RK, McCarter JP (2004) Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes. Nucleic Acids Res 32:D423–D426

    Article  PubMed  CAS  Google Scholar 

  • Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L, Wang J (2006) WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 34:W293–W297

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

J.J. has a Ph. D grant funded by Ghent University (BOF) and B.V. has a postdoctoral grant from Ghent University (BOF). Work at Washington University School of Medicine was supported by NIH-NIAID research grant AI 46593.

Author information

Authors and Affiliations

  1. Department of Molecular Biotechnology, Faculty of Bioscience Engineering, Ghent University, Coupure links 653, 9000, Ghent, Belgium

    Joachim Jacob, Bartel Vanholme & Godelieve Gheysen

  2. Genome Sequencing Center, Washington University School of Medicine, 4444 Forest Park Boulevard, St Louis, MO, USA

    Makedonka Mitreva

Authors
  1. Joachim Jacob
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Makedonka Mitreva
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bartel Vanholme
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Godelieve Gheysen
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Godelieve Gheysen.

Additional information

Communicated by S. Hohmann.

Electronic supplementary material

Below is the link to the electronic supplementary material.

438_2008_340_MOESM1_ESM.pdf

Figure A1: Comparison of the E-values obtained by BLASTx-search (Y-axis) and tBLASTx-search (X-axis). Every dot represents one unigene. Unigenes without hits in either the two searches are not represented.(76.8 KB)

438_2008_340_MOESM2_ESM.pdf

Figure A2: Density lines of the calculated total G+C content (blue line), GC1 (red), GC2 (green) and GC3 (orange) content of the coding sequence part of the unigenes, based on FrameD translation predictions.(174 KB)

438_2008_340_MOESM3_ESM.pdf

Figure A3: Alignment of five R. similis unigenes (first sequence) with the M. incognita EST with strongest homology on protein level (second sequence) and C. elegans EST with strongest homology on protein level (third sequence). Conserved sequence features of the trans-spliced leader sequences are indicated with black boxes, the start ATG codon is shaded in gray. (40.6 KB)

438_2008_340_MOESM4_ESM.pdf

Figure A4: Detection of unigenes with a G+C content of 16%, compared to the average G+C content of the majority of the unigenes. A. The density line shows normal distribution, except for a bias at the left handed side, indicated by the dashed line. B. This bias, indicated by the dashed line, can also be observed in the ‘QQ-normal plot’ (line indicates the normal distribution). C. When the total unigene set is split up into the outliers with lower G+C content (1) and the remaining unigenes (2), this bias from the normal distribution is removed. D. The absence of any bias from the normal distribution can also be observed when the QQ-normal plot is constructed for both subsets, i.e. the outliers with lower G+C content (1) and the remaining unigenes (2). (210 KB)

Supplementary material A5 (TXT 52.7 KB)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Jacob, J., Mitreva, M., Vanholme, B. et al. Exploring the transcriptome of the burrowing nematode Radopholus similis . Mol Genet Genomics 280, 1–17 (2008). https://doi.org/10.1007/s00438-008-0340-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00438-008-0340-7

Keywords

Search

Navigation