RT Journal Article SR Electronic T1 Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata JF bioRxiv FD Cold Spring Harbor Laboratory SP 207746 DO 10.1101/207746 A1 Mingshuang Wang A1 Huilan Fu A1 Xing-Xing Shen A1 Ruoxin Ruan A1 Nicholas Pun A1 Jianping Xu A1 Hongye Li A1 Antonis Rokas YR 2017 UL http://biorxiv.org/content/early/2017/10/31/207746.abstract AB The tangerine pathotype of the ascomycete fungus Alternaria alternata is the causal agent of citrus brown spot, which can result in significant losses of both yield and marketability for tangerines and tangerine hybrids worldwide. A conditionally dispensable chromosome (CDC), which harbors the host-selective ACT toxin gene cluster, is required for tangerine pathogenicity of A. alternata. To understand the genetic makeup and evolution of the tangerine pathotype CDC, we analyzed the function and evolution of the CDC genes present in the A. alternata Z7 strain. The 1.84Mb long CDC contains 512 predicted protein-coding genes, which are enriched in functional categories associated with ‘metabolic process’ (132 genes, p-value = 0.00192) including ‘oxidation-reduction process’ (48 genes, p-value = 0.00021) and ‘lipid metabolic process’ (11 genes, p-value = 0.04591). Relatively few of the CDC genes can be classified as CAZymes (13), kinases (3) and transporters (20). Differential transcriptome analysis of H2O2 treatment and control conditions revealed that 29 CDC genes were significantly up-regulated and 14 were significantly down-regulated, suggesting that CDC genes may play a role in coping with oxidative stress. Evolutionary analysis of the 512 CDC proteins showed that their evolutionary conservation tends to be restricted within the genus Alternaria and that the CDC genes evolve faster than genes in the essential chromosomes. Interestingly, phylogenetic analysis suggested that the genes of 13 enzymes and one sugar transporter residing in the CDC were likely horizontally transferred from distantly related species. Among these genes, 5 were likely transferred as a physically linked cluster of genes from Cryptococcus (Basidiomycota) or Penicillium (Eurotiomycetes) and another 4 genes might have been transferred from Colletotrichum (Sordariomycetes). One carboxylesterase gene was transferred from bacteria but functionally knocking out this gene did not affect the pathogenicity of the Z7 strain. These results provide new insights into the function and evolution of CDC genes in Alternaria.