Genomic and transcriptomic analyses of the tangerine pathotype of Alternaria alternata in response to oxidative stress

Abstract

The tangerine pathotype of Alternaria alternata produces the A. citri toxin (ACT) and is the causal agent of citrus brown spot that results in significant yield losses worldwide. Both the production of ACT and the ability to detoxify reactive oxygen species (ROS) are required for A. alternata pathogenicity in citrus. In this study, we report the 34.41 Mb genome sequence of strain Z7 of the tangerine pathotype of A. alternata. The host selective ACT gene cluster in strain Z7 was identified, which included 25 genes with 19 of them not reported previously. Of these, 10 genes were present only in the tangerine pathotype, representing the most likely candidate genes for this pathotype specialization. A transcriptome analysis of the global effects of H2O2 on gene expression revealed 1108 up-regulated and 498 down-regulated genes. Expressions of those genes encoding catalase, peroxiredoxin, thioredoxin and glutathione were highly induced. Genes encoding several protein families including kinases, transcription factors, transporters, cytochrome P450, ubiquitin and heat shock proteins were found associated with adaptation to oxidative stress. Our data not only revealed the molecular basis of ACT biosynthesis but also provided new insights into the potential pathways that the phytopathogen A. alternata copes with oxidative stress.

A Major Facilitator Superfamily Transporter-Mediated Resistance to Oxidative Stress and Fungicides Requires Yap1, Skn7, and MAP Kinases in the Citrus Fungal Pathogen Alternaria alternata

“…The full-length AaMFS19 gene sequence was identified from the completed genome sequence of A . alternata [41] and was amplified by PCR with the primers from genomic DNA. Fungal DNA was purified using a DNeasy Plant kit (Qiagen).…”

Genomic features and evolution of the conditionally dispensable chromosome in the tangerine pathotype of Alternaria alternata

“…B). Besides A .alternata Z7 (the tangerine pathotype), this cluster is also present in the Japanese pear pathotype and the strawberry pathotype (Wang et al ., ); thus we infer that the HGT events occurred before the divergence of the Z7 strain from the other Alternaria pathotypes examined and not after. The four HGT genes encode an acyl‐CoA dehydrogenase, a 3‐hydroxy‐3‐methylglutaryl (HMG)‐CoA hydrolase, a polyketide synthase and a cytochrome P450 (Table ).…”

“…Based on comparisons with proteins in the PHI database, 13 CDCs proteins are related to pathogenicity (Table ). Finally, the CDCs contained only one secondary metabolite gene cluster, the ACT toxin biosynthetic gene cluster present only in the tangerine pathotype of A. alternata , which has been described in detail previously (Wang et al ., ).…”

“…To explore the evolutionary origin of the Z7 CDCs, we compared the sequence similarity (calculated by % BLAST identity score * % query coverage) of each of the 254 CDC and EC proteins to the protein sequences from the genomes of other species in the Dothideomycetes. In the species phylogeny, Alternaria species are grouped into three clades (I , II, III), which coincides with a previously constructed phylogeny based on 200 conserved single‐copy orthologues (Wang et al ., ). Proteins in the Z7 EC showed a very high sequence similarity values (median > 75%, average = 81.0%) to proteins in other Dothideomycetes while proteins in the Z7 CDCs showed a wide range of sequence similarity values (median > 35%, average = 40.4%) to proteins in other Dothideomycetes (Fig.…”

“…The ACT toxin is essential for the pathogenicity of A. alternata Z7 to citrus leaves, the synthesis of which is predicted to be controlled by a cluster composed of about 25 genes (Wang et al ., ). The ACT toxin gene cluster is only located in the CDC and most of their genes have multiple copies (Miyamoto et al ., , ; Wang et al ., ). Surprisingly, 4/25 of the ACT cluster genes contained in the Z7 CDC strain are always grouped together with sequences from the unrelated Colletotrichum (Sordariomycetes) in their gene phylogenies (Fig.…”