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Molecular Genetics and Genomics

, Volume 273, Issue 1, pp 20–32 | Cite as

Elicitin genes in Phytophthora infestans are clustered and interspersed with various transposon-like elements

  • Rays H. Y. Jiang
  • Angus L. Dawe
  • Rob Weide
  • Marjo van Staveren
  • Sander Peters
  • Donald L. Nuss
  • Francine GoversEmail author
Original Paper

Abstract

Sequencing and annotation of a contiguous stretch of genomic DNA (112.3 kb) from the oomycete plant pathogen Phytophthora infestans revealed the order, spacing and genomic context of four members of the elicitin (inf) gene family. Analysis of the GC content at the third codon position (GC3) of six genes encoded in the region, and a set of randomly selected coding regions as well as random genomic regions, showed that a high GC3 value is a general feature of Phytophthora genes that can be exploited to optimize gene prediction programs for Phytophthora species. At least one-third of the annotated 112.3-kb P. infestans sequence consisted of transposons or transposon-like elements. The most prominent were four Tc3/gypsy and Tc1/copia type retrotransposons and three DNA transposons that belong to the Tc1/mariner, Pogo and PiggyBac groups, respectively. Comparative analysis of other available genomic sequences suggests that transposable elements are highly heterogeneous and ubiquitous in the P. infestans genome.

Keywords

Class I element Class II element Late blight CHROMO domain 

Notes

Acknowledgments

We are grateful to Sharmili Mathur for expert technical assistance, Steve Whisson for providing the BAC library and filters, Grardy van den Berg for screening the BAC library, and Pierre de Wit for critically reading the manuscript. This work was financially supported by NWO-Aspasia Grant No. 015.000.057 and USDA Cooperative Agreement No. 58-8230-6-081. The authors acknowledge Syngenta for access to the Syngenta Phytophthora Consortium EST Database, and the Broad Institute and the DOE Joint Genome Institute for depositing random genomic sequences of P. infestans and P. sojae, respectively, in the NCBI trace file archive

Supplementary material

Table S1 Codon usage and 3rd position GC frequency in 79 Phytophthora infestans genes

438_2005_1114_ESM_supp.pdf (101 kb)
(PDF 101 KB)

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Copyright information

© Springer-Verlag 2005

Authors and Affiliations

  • Rays H. Y. Jiang
    • 1
  • Angus L. Dawe
    • 2
  • Rob Weide
    • 1
  • Marjo van Staveren
    • 3
  • Sander Peters
    • 3
  • Donald L. Nuss
    • 4
  • Francine Govers
    • 1
    Email author
  1. 1.Plant Sciences Group, Laboratory of Phytopathology, Graduate School of Experimental Plant SciencesWageningen UniversityWageningenThe Netherlands
  2. 2.Biology DepartmentNew Mexico State UniversityLas CrucesUSA
  3. 3.GreenomicsPlant Research InternationalWageningenThe Netherlands
  4. 4.Center for Biosystems Research, University of Maryland Biotechnology InstituteUSA

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