Molecular Genetics and Genomics

, Volume 280, Issue 1, pp 1–17

Exploring the transcriptome of the burrowing nematode Radopholus similis

  • Joachim Jacob
  • Makedonka Mitreva
  • Bartel Vanholme
  • Godelieve Gheysen
Original Paper

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.

Keywords

Expressed sequence tag analysis Trans-spliced leader Parasitism G + C content Wolbachia Endoparasitic migratory nematode 

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

Supplementary material

438_2008_340_MOESM1_ESM.pdf (77 kb)
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 (174 kb)
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 (41 kb)
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 (210 kb)
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)
438_2008_340_MOESM5_ESM.txt (53 kb)
Supplementary material A5 (TXT 52.7 KB)

Copyright information

© Springer-Verlag 2008

Authors and Affiliations

  • Joachim Jacob
    • 1
  • Makedonka Mitreva
    • 2
  • Bartel Vanholme
    • 1
  • Godelieve Gheysen
    • 1
  1. 1.Department of Molecular Biotechnology, Faculty of Bioscience EngineeringGhent UniversityGhentBelgium
  2. 2.Genome Sequencing CenterWashington University School of MedicineSt LouisUSA

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