Open Access Research article

De novo genome assembly of the soil-borne fungus and tomato pathogen Pyrenochaeta lycopersici

Maria Aragona1, Andrea Minio2, Alberto Ferrarini2, Maria Teresa Valente1, Paolo Bagnaresi3, Luigi Orrù3, Paola Tononi2, Gianpiero Zamperin2, Alessandro Infantino1, Giampiero Valè34, Luigi Cattivelli3 and Massimo Delledonne2*

Author Affiliations

1 Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di Ricerca per la Patologia vegetale, Via C. G. Bertero 22, 00156 Roma, Italy

2 Dipartimento di Biotecnologie, Università degli Studi di Verona, Strada le Grazie, 15, 37134 Verona, Italy

3 Consiglio per la ricerca e la sperimentazione in agricoltura, Centro di Ricerca per la Genomica e la post genomica animale e vegetale, Via S. Protaso 302, 29017 Fiorenzuola d’Arda (PC), Italy

4 Consiglio per la ricerca e la sperimentazione in agricoltura, Unità di Ricerca per la Risicoltura, S.S. 11 per Torino Km 2,5, 13100 Vercelli, Italy

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BMC Genomics 2014, 15:313  doi:10.1186/1471-2164-15-313

Published: 27 April 2014

Additional files

Additional file 1: Figure S1:

Genome assembly statistics with Velvet at different k-mer length. A threshold 200 bp was set as the lowest accepted contig length. a) Number of assembled contigs. b) Maximum length of the assembled contigs. c) N50 of the assembly. d) Total sum of bases assembled in the contigs. Figure S2. Most Represented Species in Blast results. The chart reports, for the most represented species, the number of blast hits for P. lycopersici transcripts. Figure S3. Most Represented GO categories. The chart reports the number of the most represented GO categories among the assignments to P. lycopersici transcripts regarding: A) Process; B) Molecular Function. Figure S4. Comparison with Fusarium oxysporum. Homology regions at aminoacidic level are reported for each chromosome of F. oxysporum, in a vertical column, with colors representing the assembled contigs of P. lycopersici.

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Additional file 2: Table S1:

Identified CEGMA ortholog genes. Table S2. Results of identification of major membrane transporter families domains in P. lycopersici and other 9 published transcriptomes. Table S3. Summary counts peptidase of homologs found in P. lycopersici transcriptome and in 9 published fungi transcriptomes. Table S4. Identification results of Heterokaryon Incompatibility proteins related domains in P. lycopersici (highlighted) and comparison with other fungal genomes. Table S5. Results of CAZyme domains identification comparison between P. lycopersici (highlighted) and other fungal genomes. Table S6. Carbohydrate-degrading enzymes in P. lycopersici (highlighted) and other Ascomycetes.

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Additional file 3:

Genome annotation. This XLS document contains the annotation of P. lycopersici genome.

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