TY - JOUR
T1 - Genomic characterization of the conditionally dispensable chromosome in Alternaria arborescens provides evidence for horizontal gene transfer.
AU - Hu, Jinnan
AU - Chen, Chenxi
AU - Peever, Tobin
AU - Dang, H.
AU - Lawrence, Christopher
AU - Mitchell, Thomas
N1 - Funding Information:
We are grateful to Dr. R.C. Venu at The Ohio State University (OSU) for preparing the sequencing library and the OSU Molecular Cellular Imaging Center (MCIC) for performing Illumina sequencing. We thank Drs. Kun Huang and Hideaki Kikuchi at the OSU Department of Biomedical Informatics for providing access to the high performance computing cluster. This work was supported by grant 2009–012 from the Ohio Agricultural Research and Development Center’s Research Enhancement Competitive Grants Program (SEED).
PY - 2012
Y1 - 2012
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=84860533256&partnerID=8YFLogxK
U2 - 10.1186/1471-2164-13-171
DO - 10.1186/1471-2164-13-171
M3 - Article
C2 - 22559316
AN - SCOPUS:84860533256
SN - 1471-2164
VL - 13
JO - BMC genomics
JF - BMC genomics
ER -