Open Access Research article

The CAZyome of Phytophthora spp.: A comprehensive analysis of the gene complement coding for carbohydrate-active enzymes in species of the genus Phytophthora

Manuel D Ospina-Giraldo*, John G Griffith, Emma W Laird and Christina Mingora

Author Affiliations

29 Kunkel, Biology Department, Lafayette College, Easton, PA 18042, USA

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BMC Genomics 2010, 11:525  doi:10.1186/1471-2164-11-525

Published: 28 September 2010

Additional files

Additional file 1:

CAZy genes in P. infestans. CAZyme-coding homologs in P. infestans organized by their respective CAZy superfamily. 1Numbers represent intron sizes; "multiple" refers to the fact that more than 9 introns were present in the gene model. 2Cellular localization predicted by SecretomeP, SignalP, or TargetP algorithms. ND, not determined.

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Additional file 2:

CAZy genes in P. sojae. CAZyme-coding homologs in P. sojae organized by their respective CAZy superfamily. 1Numbers represent intron sizes; "multiple" refers to the fact that more than 9 introns were present in the gene model. 2Most likely cellular localization predicted by SecretomeP, SignalP, or TargetP algorithms. ND, not determined.

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Additional file 3:

CAZy genes in P. ramorum. CAZyme-coding homologs in P. ramorum organized by their respective CAZy superfamily. 1Numbers represent intron sizes; "multiple" refers to the fact that more than 9 introns were present in the gene model. 2Most likely cellular localization predicted by SecretomeP, SignalP, or TargetP algorithms. ND, not determined.

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Additional file 4:

Phytophthora CE orthologs. Phytophthora CE orthologs as determined using the Phylogenetic Resources for the Interpretation of Genomes (PHRINGE). All, but one, of the CE homologs had orthologs in both P. sojae and P. ramorum genomes. In most cases, more than one orthologous gene was found in each of the three Phytophthora species.

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Additional file 5:

Phytophthora GH orthologs. Phytophthora GH orthologs as determined using the Phylogenetic Resources for the Interpretation of Genomes (PHRINGE). In most cases, more than one orthologous gene was found in each of the three Phytophthora species. Two hundred fourteen GH-coding genes had orthologs in both P. sojae and P. ramorum. Three putative GH-coding genes had an ortholog only in P. ramorum, while seven other had an ortholog in P. sojae only. The remaining 20 genes did not appear to have orthologs in either genome.

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Additional file 6:

Phytophthora GT orthologs. Phytophthora GT orthologs as determined using the Phylogenetic Resources for the Interpretation of Genomes (PHRINGE). In most cases, more than one orthologous gene was found in each of the three Phytophthora species. A total of 72 members had orthologs in both, P. sojae and P. ramorum genomes while three had orthologs in P. sojae only.

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Additional file 7:

Phytophthora PL orthologs. Phytophthora PL orthologs. Phytophthora PL orthologs as determined using the Phylogenetic Resources for the Interpretation of Genomes (PHRINGE). In most cases, more than one orthologous gene was found in each of the three Phytophthora species. A total of 56 (out of 59) P. infestans PL-coding genes had orthologs either in both, P. sojae and P. ramorum (53), or in P. ramorum only (3).

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