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Comparative Study
. 2000 May;123(1):243-54.
doi: 10.1104/pp.123.1.243.

Comparative analysis of expressed sequences in Phytophthora sojae

D Qutob  1 , P T Hraber, B W Sobral, M Gijzen
Affiliations
Comparative Study

Comparative analysis of expressed sequences in Phytophthora sojae

D Qutob et al. Plant Physiol. 2000 May.

Abstract

Phytophthora sojae (Kaufmann and Gerdemann) is an oomycete that causes stem and root rot on soybean (Glycine max L. Merr) plants. We have constructed three cDNA libraries using mRNA isolated from axenically grown mycelium and zoospores and from tissue isolated from plant hypocotyls 48 h after inoculation with zoospores. A total of 3,035 expressed sequence tags (ESTs) were generated from the three cDNA libraries, representing an estimated 2,189 cDNA transcripts. The ESTs were classified according to putative function based on similarity to known proteins, and were analyzed for redundancy within and among the three source libraries. Distinct expression patterns were observed for each library. By analysis of the percentage G+C content of the ESTs, we estimate that two-thirds of the ESTs from the infected plant library are derived from P. sojae cDNA transcripts. The ESTs originating from this study were also compared with a collection of Phytophthora infestans ESTs and with all other non-human ESTs to assess the similarity of the P. sojae sequences to existing EST data. This collection of cDNA libraries, ESTs, and accompanying annotation will provide a new resource for studies on oomycetes and on soybean responses to pathogen challenge.

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Figures

Figure 1
Figure 1
Frequency distributions of ESTs from each of the source cDNA libraries according to P-value scores returned from BLASTX version 1.4.11 searches.
Figure 2
Figure 2
Classification of ESTs according to putative biological function. Protein matches resulting from the BLASTX searches were assigned to one of seven functional categories for life cycle comparisons. Shown is the percentage frequency of clones in each category for the total set of ESTs from each source library.
Figure 3
Figure 3
Distribution of ESTs on the basis of percentage G+C content. The ESTs were grouped in 1% increments of percentage G+C content and the resulting distributions plotted. Source cDNA library is indicated for each histogram.
Figure 4
Figure 4
Assessment of EST redundancy in each of the three cDNA libraries by contiguous sequence assembly analysis. Contigs that consist of one sequence are considered singletons, whereas contigs comprised of two or more sequences are classified as redundant ESTs. Shown is a plot of the frequency of singleton and redundant ESTs for each of the source libraries.
Figure 5
Figure 5
Comparative analysis of ESTs derived from each of the source cDNA libraries using TBLASTX, version 2.0.6. P. sojae and soybean EST sequences generated in this study were compared with two distinct data sets, one consisting of P. infestans mycelium ESTs and another, larger data set of non-human ESTs from all taxa, as described in “Materials and Methods.” Raw scores from the best match to each target are shown from infected soybean (top), mycelium (middle), and zoospore (bottom) libraries. The black circles indicate the 10 sequences from each library that the had the greatest difference between scores, but where neither score was zero, as shown in Table II.
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References

    1. Adams MD, Kelley JM, Gocayne JD, Dubnick M, Polymeropoulos MH, Xiao H, Merril CR, Wu A, Olde B, Moreno RF, Kerlavage AR, McCombie WR, Venter JC. Complementary DNA sequencing: expressed sequence tags and human genome project. Science. 1991;252:1651–1656. - PubMed
    1. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–410. - PubMed
    1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, Miller W, Lipman DJ. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. - PMC - PubMed
    1. Anderson TR, Buzzell RI. Diversity and frequency of races of Phytophthora megasperma f. sp. glycinea in soybean fields in Essex County, Ontario, 1980–1989. Plant Dis. 1992;76:587–589.
    1. Dellaporta S, Woods H, Hicks J. A plant DNA mini-preparation: version II. Plant Mol Biol Rep. 1983;1:19–21.

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