Open Access Highly Accessed Research article

RNA-Seq analysis reveals new gene models and alternative splicing in the fungal pathogen Fusarium graminearum

Chunzhao Zhao1234, Cees Waalwijk12, Pierre J G M de Wit25, Dingzhong Tang3 and Theo van der Lee12*

Author Affiliations

1 Plant Research International, P.O. Box 6708 PB, Wageningen, The Netherlands

2 Graduate School Experimental Plant Sciences, Wageningen, The Netherlands

3 State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China

4 Graduate University of Chinese Academy of Sciences, Beijing, 100049, China

5 Wageningen University, Laboratory of Phytopathology, P.O. Box 6708 PB, Wageningen, The Netherlands

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BMC Genomics 2013, 14:21  doi:10.1186/1471-2164-14-21

Published: 16 January 2013

Additional files

Additional file 1:

Gene expression analysis in wt PH-1. Expression analysis of the 13321 predicted genes in wt PH-1 after incubation in liquid CM medium for 30 h.

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Additional file 2:

Gene expression analysis in mutant ebr1. Expression analysis of the 13321 predicted genes in mutant ebr1 after incubation in liquid CM medium for 30 h.

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Additional file 3:

PDF file containing all supplementary figures and their legends.

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Additional file 4:

Incorrectly annotated genes that have been revised in the MIPS F. graminearum database. 278 genes that were incorrectly annotated in Broad F. graminearum database have already been revised in MIPS F. graminearum database.

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Additional file 5:

Genes with incorrect intron predictions. 119 genes with incorrect intron predictions were identified and revised.

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Additional file 6:

Genes with novel introns. 40 genes with novel introns were identified and revised.

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Additional file 7:

Genes with incorrect splice sites. 164 genes (186 introns) with incorrectly predicted splice sites were identified and revised.

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Additional file 8:

Genes with intron retention. 211 genes with intron retention were shown.

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Additional file 9:

Genes with alternative 5′ splicing. 21 genes with alternative 5′ splicing were shown.

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Additional file 10:

Genes with alternative 3′ splicing. 12 genes with alternative 3′ splicing were shown.

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Additional file 11:

Genes with exon skipping. 4 genes with exon skipping were shown.

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Additional file 12:

Genes with non-canonical splice sites. Non-canonical splice sites were identified in 28 genes.

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Additional file 13:

nTARs identified in intergenic regions. 2459 nTARs were identified in intergenic regions. The expression levels of these nTARs and their orthologs in F. oxysporum and F. verticillioides were analyzed.

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Additional file 14:

Identification of 5′ UTRs. 5′ UTRs of 5951 genes were determined by RNA-Seq data.

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Additional file 15:

Identification of 3′ UTRs. 3′ UTRs of 6405 genes were determined by RNA-Seq data.

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Additional file 16:

Primers used in this study.

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