Skip to main content
SpringerLink
Log in

Transcriptomes of Plant-Parasitic Nematodes

  • Chapter
  • First Online:
Genomics and Molecular Genetics of Plant-Nematode Interactions

Abstract

Undoubtedly, transcriptomic analysis has contributed significantly to the understanding of the molecular basis of parasitism by plant-parasitic nematodes. In this chapter we will review the contributions by this approach. We will discuss the generation of EST sequences and their characteristics. We provide a summary of generally applied bioinformatics processing step to reach the goal of increasing the understanding of the parasitism process at the molecular level and host-parasite interactions. Herewith, useful tools and software are being referenced to. The selection of tools described in this chapter is not all inclusive, but rather reflects those used by the authors at the time of writing. We discuss the results obtained from a pan-phylum comparison of EST data, before ending with thoughts about future developments in the field of transcriptomics.

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

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 259.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 329.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 329.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abad P, Gouzy J, Aury J-M, Castagnone-Sereno P, Danchin EGJ, Deleury E, Perfus-Barbeoch L, Anthouard V, Artiguenave F, Blok VC, Caillaud M-C, Coutinho PM, Dasilva C, De Luca F, Deau F, Esquibet M, Flutre T, Goldstone JV, Hamamouch N, Hewezi T, Jaillon O, Jubin C, Leonetti P, Magliano M, Maier TR, Markov GV, McVeigh P, Pesole G, Poulain J, Robinson-Rechavi M, Sallet E, Segurens B, Steinbach D, Tytgat T, Ugarte E, van Ghelder C, Veronico P, Baum TJ, Blaxter M, Bleve-Zacheo T, Davis EL, Ewbank JJ, Favery B, Grenier E, Henrissat B, Jones JT, Laudet V, Maule AG, Quesneville H, Rosso M-N, Schiex T, Smant G, Weissenbach J, Wincker P (2008) Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotech 26:909–915

    Article  CAS  Google Scholar 

  • Audic S, Claverie JM (1997) The significance of digital gene expression profiles. Genome Res 7:986–995

    PubMed  CAS  Google Scholar 

  • Bellafiore S, Shen Z, Rosso M-N, Abad P, Shih P, Briggs SP (2008) Direct identification of the Meloidogyne incognita secretome reveals proteins with host cell reprogramming potential. PLoS Pathog 4:e1000192

    Article  PubMed  Google Scholar 

  • Bendtsen JD, Nielsen H, von Heijne G, Brunak S (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795

    Article  PubMed  Google Scholar 

  • Bird DM, Opperman CH (2009) The secret(ion) life of worms. Genome Biol 10:205

    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 

  • Curtis RH (2007) Plant parasitic nematode proteins and the host parasite interaction. Brief funct Genomic Proteomic 6:50–58

    Article  PubMed  CAS  Google Scholar 

  • Dautova M, Rosso MN, Abad P, Gommers FJ, Bakker J, Smant G (2001) Single pass cDNA sequencing—a powerful tool to analyse gene expression in preparasitic juveniles of the southern root-knot nematode Meloidogyne incognita. Nematology 3:129–139

    Article  CAS  Google Scholar 

  • Davis EL, Hussey RS, Baum TJ (2004) Getting to the roots of parasitism by nematodes. Trends Parasitol 20:134–141

    Article  PubMed  Google Scholar 

  • De Boer JM, Overmars H, Pomp HR, Davis EL, Zilverentant JF, Goverse A, Smant G, Stokkermans J, Hussey RS, Gommers FJ, Bakker J, Schots A (1996a) Production an characterisation of monoclonal antibodies to antigens from second stage juveniles of the potato cyst nematode Globodera rostochiensis. Fund App Nematol 19:545–554

    Google Scholar 

  • De Boer JM, Smant G, Goverse A, Davis EL, Overmars HA, Pomp H, van Gent-Pelzer M, Zilverentant JF, Stokkermans JP, Hussey RS, Gommers FJ, Bakker J, Schots A (1996b) Secretory granule proteins from the subventral esophageal glands of the potato cyst nematode identified by monoclonal antibodies to a protein fraction from second-stage juveniles. Mol Plant Microbe Interact 9:39–46

    Article  Google Scholar 

  • De Boer JM, McDermott JP, Davis EL, Hussey RS, Smant G, Baum TJ (2002) Cloning of a putative pectate lyase gene expressed in the subventral esophageal glands of Heterodera glycines. J Nematol 33:9–11

    Google Scholar 

  • Ding X, Shields J, Allen R, Hussey RS (2000) Molecular cloning and characterisation of a venom allergen AG5-like cDNA from Meloidogyne incognita. Int J Parasitol 30:77–81

    Article  PubMed  CAS  Google Scholar 

  • Doyle EA, Lambert KN (2002) Cloning and characterization of an esophageal-gland-specific pectate lyase from the root-knot nematode Meloidogyne javanica. Mol Plant Microbe Interact 15:549–556

    Article  PubMed  CAS  Google Scholar 

  • Droege M, Hill B (2008) The genome sequencer FLX(TM) system–longer reads, more applications, straight forward bioinformatics and more complete data sets. J Biotechnol 136:3–10

    Article  PubMed  CAS  Google Scholar 

  • Elling AA, Davis EL, Hussey RS, Baum TJ (2007a) Active uptake of cyst nematode parasitism proteins into the plant cell nucleus. Int J Parasitol 37:1269–1279

    Article  CAS  Google Scholar 

  • Elling A, Mitreva M, Recknor J, Gai X, Martin J, Maier T, McDermott J, Hewezi T, McK Bird D, Davis E, Hussey R, Nettleton D, McCarter J, Baum T (2007b) Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines. Genome Biol 8:R211

    Article  Google Scholar 

  • Elling AA, Mitreva M, Gai X, Martin J, Recknor J, Davis EL, Hussey RS, Nettleton D, McCarter JP, Baum TJ (2009) Sequence mining and transcript profiling to explore cyst nematode parasitism. BMC Genomics 10:58

    Article  PubMed  Google Scholar 

  • Fioretti L, Warry A, Porter A, Haydock P, Curtis R (2001) Isolation and localisation of an annexin gene (gp-nex) from the potato cyst nematode, Globodera pallida. Nematology 3:45–54

    Article  CAS  Google Scholar 

  • Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS (2001) Molecular characterisation and expression of two venom allergen-like protein genes in Heterodera glycines. Int J Parasitol 31:1617–1625

    Article  PubMed  CAS  Google Scholar 

  • Gao B, Allen R, Maier T, Davis EL, Baum TJ, Hussey RS (2003) The parasitome of the phytonematode Heterodera glycines. Mol Plant Microbe Interact 16:720–726

    Article  PubMed  CAS  Google Scholar 

  • Giebel J (1973) Biochemical mechanisms of plant resistance to nematodes: A review. J Nematol 6:175–184

    Google Scholar 

  • Givnish TJ, Evans TM, Zjhra ML, Patterson TB, Berry PE, Sytsma KJ (2000) Molecular evolution, adaptive radiation, and geographic diversification in theamphiatlantic family Rapateaceae: evidence from ndhF sequences and morphology. Int J Org Evol 54:1915–1937

    CAS  Google Scholar 

  • Goellner M, Smant G, de Boer JM, Baum TJ, Davis EL (2000) Isolation of beta-1,4-endoglucanase genes from Globodera tabacum and their expression during parasitism. J Nematol 32:154–165

    PubMed  CAS  Google Scholar 

  • Haegeman A, Vanholme B, Jacob J, Vandekerckhove TTM, Claeys M, Borgonie G, Gheysen G (2009) An endosymbiotic bacterium in a plant-parasitic nematode: Member of a new Wolbachia supergroup. Int J Parasitol 39:1045–1054

    Article  PubMed  Google Scholar 

  • Harris TW, Antoshechkin I, Bieri T, Blasiar D, Chan J, Chen WJ, De La Cruz N, Davis P, Duesbury M, Fang R, Fernandes J, Han M, Kishore R, Lee R, Muller H-M, Nakamura C, Ozersky P, Petcherski A, Rangarajan A, Rogers A, Schindelman G, Schwarz EM, Tuli MA, Van Auken K, Wang D, Wang X, Williams G, Yook K, Durbin R, Stein LD, Spieth J, Sternberg PW (2010) WormBase: a comprehensive resource for nematode research. Nucleic Acids Res 38:D463–D467

    Article  PubMed  CAS  Google Scholar 

  • Huang GZ, Gao BL, Maier T, Allen R, Davis EL, Baum TJ, Hussey RS (2003) A profile of putative parasitism genes expressed in the esophageal gland cells of the root-knot nematode Meloidogyne incognita. Mol Plant Microbe Interact 16:376–381

    Article  PubMed  CAS  Google Scholar 

  • Huang GZ, Dong RH, Maier T, Allen R, Davis EL, Baum TJ, Hussey RS (2004) Use of solid-phase subtractive hybridization for the identification of parasitism gene candidates from the root-knot nematode Meloidogyne incognita. Mol Plant Pathol 5:217–222

    Article  PubMed  CAS  Google Scholar 

  • Jacob J (2009) Plant-parasitic nematodes: from genomics to functional analysis of parasitism genes. PhD Thesis, Ghent University, Faculty of Bioscience Engineering, Ghent, Belgium

    Google Scholar 

  • Jacob J, Mitreva M, Vanholme B, Gheysen G (2008) Exploring the transcriptome of the burrowing nematode Radopholus similis. Mol Genet Genomics 280:1–17, PMID: 18386064

    Article  PubMed  CAS  Google Scholar 

  • Jacob J, Vanholme B, Van Leeuwen T, Gheysen G (2009) A unique genetic code change in the mitochondrial genome of the parasitic nematode Radopholus similis. BMC Res Notes 2:192

    Article  PubMed  Google Scholar 

  • Jang CS, Jung JH, Yim WC, Lee BM, Seo YW, Kim W (2007) Divergence of genes encoding non-specific lipid transfer proteins in the poaceae family. Mol Cells 24:215–223

    PubMed  CAS  Google Scholar 

  • Jones JT, Furlanetto C, Kikuchi T (2003) Horizontal gene transfer from bacteria and fungi as a driving force in the evolution of plant parasitism in nematodes. Nematology 7:641–646

    Article  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 

  • Karim N, Jones J, Okada H, Kikuchi T (2009) Analysis of expressed sequence tags and identification of genes encoding cell-wall-degrading enzymes from the fungivorous nematode Aphelenchus avenae. BMC Genomics 10:525

    Article  PubMed  Google Scholar 

  • Kikuchi T, Shibuya H, Jones JT (2005) Molecular and biochemical characterization of an endo-beta-1,3-glucanase from the pinewood nematode Bursaphelenchus xylophilus acquired by horizontal gene transfer from bacteria. Biochem J 389:117–125

    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 155:9–17

    Article  PubMed  CAS  Google Scholar 

  • Kocher TD (2004) Adaptive evolution and explosive speciation: the cichlid fish model. Nat Rev Genet 5:288–298

    Article  PubMed  CAS  Google Scholar 

  • Lambert KN, Allen KD, Sussex IM (1999) Cloning and characterization of an esophageal-gland-specific chorismate mutase from the phytoparasitic nematode Meloidogyne javanica. Mol Plant Microbe Interact 12:328–336

    Article  PubMed  CAS  Google Scholar 

  • Lilley CJ, Urwin PE, Atkinson HJ (1999) Characterization of plant nematode genes: identifying targets for a transgenic defence. Parasitology 118:S63–S72

    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

    Article  PubMed  CAS  Google Scholar 

  • Mardis ER (2008) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  PubMed  CAS  Google Scholar 

  • Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen Y-J, Chen Z, Dewell SB, Du L, Fierro JM, Gomes XV, Godwin BC, He W, Helgesen S, Ho CH, Irzyk GP, Jando SC, Alenquer MLI, Jarvie TP, Jirage KB, Kim J-B, Knight JR, Lanza JR, Leamon JH, Lefkowitz SM, Lei M, Li J, Lohman KL, Lu H, Makhijani VB, McDade KE, McKenna MP, Myers EW, Nickerson E, Nobile JR, Plant R, Puc BP, Ronan MT, Roth GT, Sarkis GJ, Simons JF, Simpson JW, Srinivasan M, Tartaro KR, Tomasz A, Vogt KA, Volkmer GA, Wang SH, Wang Y, Weiner MP, Yu P, Begley RF, Rothberg JM (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature 437:376–380

    PubMed  CAS  Google Scholar 

  • Martin J, Abubucker S, Wylie T, Yin Y, Wang Z, Mitreva M (2009) Nematode.net update 2008: improvements enabling more efficient data mining and comparative nematode genomics. Nucleic Acids Res 37:D571–D578

    Article  PubMed  CAS  Google Scholar 

  • Mitreva M, Mardis ER (2009) Large-scale sequencing and analytical processing of ESTs. Methods Mol Biol 533:153–187

    Article  PubMed  CAS  Google Scholar 

  • Mitreva M, McCarter JP, Martin J, Dante M, Wylie T, Chiapelli B, Pape D, Clifton SW, Nutman TB, Waterston RH (2004a) Comparative genomics of gene expression in the parasitic and free-living nematodes Strongyloides stercoralis and Caenorhabditis elegans. Genome Res 14:209–220

    Article  Google Scholar 

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

    Article  CAS  Google Scholar 

  • Mitreva M, McCarter JP, Arasu P, Hawdon J, Martin J, Dante M, Wylie T, Xu J, Stajich JE, Kapulkin W, Clifton SW, Waterston RH, Wilson RK (2005) Investigating hookworm genomes by comparative analysis of two Ancylostoma species. BMC Genomics 6:58

    Article  PubMed  Google Scholar 

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

    Article  Google Scholar 

  • Mitreva-Dautova M, Roze E, Overmars H, de Graaff L, Schots A, Helder J, Goverse A, Bakker J, Smant G (2006) A symbiont-independent endo-1,4-beta-xylanase from the plant-parasitic nematode Meloidogyne incognita. Mol Plant Microbe Interact 19:521–529

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  Google Scholar 

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

    Google Scholar 

  • Nagaraj SH, Gasser RB, Ranganathan S (2008) Needles in the EST Haystack: Large-scale identification and analysis of Excretory-Secretory (ES) proteins in parasitic nematodes using Expressed Sequence Tags (ESTs). PLoS Negl Trop Dis 2:e301

    Article  PubMed  Google Scholar 

  • Olsen A, Skriver K (2003) Ligand mimicry? Plant-parasitic nematode polypeptide with similarity to CLAVATA3. Trends Plant Sci 8:55–57

    Article  PubMed  CAS  Google Scholar 

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

    Article  PubMed  CAS  Google Scholar 

  • Opperman CH, Bird DM, Williamson VM, Rokhsar DS, Burke M, Cohn J, Cromer J, Diener S, Gajan J, Graham S, Houfek TD, Liu Q, Mitros T, Schaff J, Schaffer R, Scholl E, Sosinski BR, Thomas VP, Windham E (2008) Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism. Proc Natl Acad Sci USA 105:14802–14807

    Article  PubMed  CAS  Google Scholar 

  • Panhuis TM, Clark NL, Swanson WJ (2006) Rapid evolution of reproductive proteins in abalone and Drosophila. Philos Trans R Soc B: Biol Sci 361:261–268

    Article  CAS  Google Scholar 

  • Parkinson J, Blaxter ML (2003) SimiTri–visualizing similarity relationships for groups of sequences. Bioinformatics 19:390–395

    Article  PubMed  CAS  Google Scholar 

  • Parkinson J, Anthony A, Wasmuth J, Schmid R, Hedley A, Blaxter M (2004a) PartiGene—constructing partial genomes. Bioinformatics 20:1398–1404

    Article  CAS  Google Scholar 

  • Parkinson J, Mitreva M, Whitton C, Thomson M, Daub J, Martin J, Hall N, Barrell B, Waterston RH, McCarter JP, Blaxter M (2004b) A transcriptomic analysis of the phylum Nematoda. Nat Genet 36:1259–1267

    Article  Google Scholar 

  • Parkinson J, Whitton C, Schmid R, Thomson M, Blaxter M (2004c) NEMBASE: a resource for parasitic nematode ESTs. Nucleic Acids Res 32:D427–D430

    Article  CAS  Google Scholar 

  • Parra G, Bradnam K, Korf I (2007) CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes. Bioinformatics 23:1061–1067

    Article  PubMed  CAS  Google Scholar 

  • Peng J, Huang CH (2006) Rh proteins vs Amt proteins: an organismal and phylogenetic perspective on CO2 and NH3 gas channels. Transfus Clin Biol 13:85–94

    Article  PubMed  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 

  • Popeijus H, Blok VC, Cardle L, Bakker E, Phillips MS, Helder J, Smant G, Jones JT (2000) Analysis of genes expressed in second stage juveniles of the potato cyst nematodes Globodera rostochiensis and G. pallida using the expressed sequence tag approach. Nematology 2:567–574

    Article  CAS  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 

  • Qin L, Overmars H, Helder J, Popeijus H, van der Voort JR, Groenink W, van Koert P, Schots A, Bakker J, Smant G (2000) An efficient cDNA-AFLP-based strategy for the identification of putative pathogenicity factors from the potato cyst nematode Globodera rostochiensis. Mol Plant Microbe Interact 13:830–836

    Article  PubMed  CAS  Google Scholar 

  • Robinson MW, Connolly B (2005) Proteomic analysis of the excretory-secretory proteins of the Trichinella spiralis L1 larva, a nematode parasite of skeletal muscle. Proteomics 5:4525–4532

    Article  PubMed  CAS  Google Scholar 

  • Rosso MN, Favery B, Piotte C, Arthaud L, De Boer JM, Hussey RS, Bakker J, Baum TJ, Abad P (1999) Isolation of a cDNA encoding a beta-1,4-endoglucanase in the root-knot nematode Meloidogyne incognita and expression analysis during plant parasitism. Mol Plant Microbe Interact 12:585–591

    Article  PubMed  CAS  Google Scholar 

  • Roze E, Hanse B, Mitreva M, Vanholme B, Bakker J, Smant G (2008) Mining the secretome of the root-knot nematode Meloidogyne chitwoodi for candidate parasitism genes. Mol Plant Pathol 9:1–10

    PubMed  CAS  Google Scholar 

  • 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 

  • Simon SA, Zhai J, Nandety RS, McCormick KP, Zeng J, Mejia D, Meyers BC (2009) Short-Read sequencing technologies for transcriptional analyses. Ann Rev Plant Biol 60:305–333

    Article  CAS  Google Scholar 

  • Smant G, Stokkermans JP, Yan Y, de Boer JM, Baum TJ, Wang X, 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. Proc Natl Acad Sci U S A 95:4906–4911

    Article  PubMed  CAS  Google Scholar 

  • Sonnhammer EL, von Heijne G, Krogh A (1998) A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol 6:175–182

    PubMed  CAS  Google Scholar 

  • Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A et al. (2003) The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biol 1:E45

    Article  PubMed  Google Scholar 

  • The Gene Ontology C (2008) The gene ontology project in 2008. Nucleic Acids Res 36:D440–D444

    Article  Google Scholar 

  • Tucker ML, Xue P, Raina A, Ehrenfried ML, Asif M, Thai VK (2005) Characterization of several Heterodera glycines mRNAs that encode small proteins with putative signal peptides. J Nematol 37:422–428

    PubMed  CAS  Google Scholar 

  • Uehara T, Kushida A, Momota Y (2001) PCR-based cloning of two beta-1,4-endoglucanases from the root-lesion nematode Pratylenchus penetrans. Nematology 3:335–41

    Article  CAS  Google Scholar 

  • Vanholme B, De Meutter J, Tytgat T, Van Montagu M, Coomans A, Gheysen G (2004) Secretions of plant-parasitic nematodes: a molecular update. Gene 332:13–27

    Article  PubMed  CAS  Google Scholar 

  • Vanholme B, Mitreva M, Van Criekinge W, Logghe M, Bird D, McCarter J, Gheysen G (2006) Detection of putative secreted proteins in the plant-parasitic nematode Heterodera schachtii. Parasitol Res 98:414–424

    Article  PubMed  Google Scholar 

  • Wang J-P, Lindsay B, Cui L, Wall PK, Marion J, Zhang J, dePamphilis C (2005) Gene capture prediction and overlap estimation in EST sequencing from one or multiple libraries. BMC Bioinformatics 6:300

    Article  PubMed  Google Scholar 

  • Wang X, Allen R, Ding X, Goellner M, Maier T, de Boer JM, Baum TJ, Hussey RS, Davis EL (2001) Signal peptide-selection of cDNA cloned directly from the esophageal gland cells of the soybean cyst nematode Heterodera glycines. Mol Plant Microbe Interact 14:536–544

    Article  PubMed  CAS  Google Scholar 

  • Wang Z, Martin J, Abubucker S, Yin Y, Gasser R, Mitreva M (2009) Systematic analysis of insertions and deletions specific to nematode proteins and their proposed functional and evolutionary relevance. BMC Evol Biol 9:23

    Article  PubMed  CAS  Google Scholar 

  • Wang Z, Abubucker S, Martin J, Wilson RK, Hawdon J, Mitreva M (2010) Characterizing Ancylostoma caninum transcriptome and exploring nematode parasitic adaptation. BMC Genomics 11:307

    Article  PubMed  Google Scholar 

  • Wasmuth JD, Blaxter ML (2004) prot4EST: translating expressed sequence tags from neglected genomes. BMC Bioinformatics 5:187

    Article  PubMed  Google Scholar 

  • Wasmuth J, Schmid R, Hedley A, Blaxter M (2008) On the extent and origins of genic novelty in the phylum Nematoda. PloS Negl Trop Dis 2:e258

    Article  PubMed  Google Scholar 

  • Wylie T, Martin J, Dante M, Mitreva M, 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 

  • Wylie T, Martin J, Abubucker S, Yin Y, Messina D, Wang Z, McCarter J, Mitreva M (2008) NemaPath: online exploration of KEGG-based metabolic pathways for nematodes. BMC Genomics 9:525

    Article  PubMed  Google Scholar 

  • Yan J, Marr TG (2005) Computational analysis of 3′-ends of ESTs shows four classes of alternative polyadenylation in human, mouse, and rat. Genome Res 15:369–375

    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:W293–297

    Article  PubMed  CAS  Google Scholar 

  • Yin Y, Martin J, Abubucker S, Wang Z, Wyrwicz L, Rychlewski L, McCarter J, Wilson R, Mitreva M (2009) Molecular determinants archetypical to the phylum Nematoda. BMC Genomics 10:114

    Article  PubMed  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Bioinformatics Training and Service facility, VIB, Rijvisschestraat 120, 9052, Gent, Belgium

    Joachim Jacob

  2. Department of Genetics, Washington University School of Medicine, Forest Park Boulevard, 4444, 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

Corresponding author

Correspondence to Joachim Jacob .

Editor information

Editors and Affiliations

  1. , Plant Pathology, Scottish Crop Research Institute, Invergowrie, Dundee, DD2 5DA, United Kingdom

    John Jones

  2. , Molecular Biotechnology, Ghent University, Coupure links 653, Ghent, 9000, Belgium

    Godelieve Gheysen

  3. , Environmental Sciences, Universidad de Castilla-La Mancha, Avda. Carlos III. s/n, Toledo, E-45071, Spain

    Carmen Fenoll

Rights and permissions

Reprints and permissions

Copyright information

© 2011 Springer Science+Business Media B.V.

About this chapter

Cite this chapter

Jacob, J., Mitreva, M. (2011). Transcriptomes of Plant-Parasitic Nematodes. In: Jones, J., Gheysen, G., Fenoll, C. (eds) Genomics and Molecular Genetics of Plant-Nematode Interactions. Springer, Dordrecht. https://doi.org/10.1007/978-94-007-0434-3_7

Download citation

Publish with us

Policies and ethics

Search

Navigation