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

BMC Genomics
Jinnan HuThomas Mitchell

Abstract

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 wa...Continue Reading

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Datasets Mentioned

BETA
AIIC00000000

Methods Mentioned

BETA
electrophoresis
Illumina sequencing
2

Software Mentioned

Primer3
FGENESH
MEGA
Nucmer
Edena
Minimus2
Codem
Illumina Genome Analyzer II
PAML suite
Automated Codon Usage Analysis Software ( ACUA

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