Open Access Open Badges Research article

Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer

Jinnan Hu1, Chenxi Chen1, Tobin Peever2, Ha Dang3, Christopher Lawrence3 and Thomas Mitchell1*

Author Affiliations

1 Department of Plant Pathology, The Ohio State University, Columbus, OH 43210, USA

2 Department of Plant Pathology, Washington State University, Pullman, WA 99164-6430, USA

3 Virginia Bioinformatics Institute, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA

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BMC Genomics 2012, 13:171  doi:10.1186/1471-2164-13-171

Published: 6 May 2012



Fungal plant pathogens cause serious agricultural losses worldwide. Alternaria arborescens is a major pathogen of tomato, with its virulence determined by the presence of a conditionally dispensable chromosome (CDC) carrying host-specific toxin genes. Genes encoding these toxins are well-studied, however the genomic content and organization of the CDC is not known.


To gain a richer understanding of the molecular determinants of virulence and the evolution of pathogenicity, we performed whole genome sequencing of A. arborescens. Here we present the de-novo assembly of the CDC and its predicted gene content. Also presented is hybridization data validating the CDC assembly. Predicted genes were functionally annotated through BLAST. Gene ontology terms were assigned, and conserved domains were identified. Differences in nucleotide usage were found between CDC genes and those on the essential chromosome (EC), including GC3-content, codon usage bias, and repeat region load. Genes carrying PKS and NRPS domains were identified in clusters on the CDC and evidence supporting the origin of the CDC through horizontal transfer from an unrelated fungus was found.


We provide evidence supporting the hypothesis that the CDC in A. arborescens was acquired through horizontal transfer, likely from an unrelated fungus. We also identified several predicted CDC genes under positive selection that may serve as candidate virulence factors.

Alternaria arborescens; Illumina sequencing; Conditionally dispensable chromosome; Horizontal gene transfer; Polyketide synthase; Host specific toxins