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Background  The Ambrosia  Fusarium  Clade phytopathogenic  Fusarium  fungi species have a symbiotic relationship with ambrosia beetles in the genus  Euwallacea  (Coleoptera: Curculionidae). Related beetle species referred to as  Euwallacea  sp. near  fornicatus  have been spread in California, USA and are recognized as the causal agents of  Fusarium  dieback, a disease that causes mortality of many plant species. Despite the importance of this fungi, no transcriptomic resources have been generated. The datasets described here represent the first ever transcripts available for these species. We focused our study on the isolated species of  Fusarium  that is associated with one of the cryptic species referred to as Kuroshio Shot Hole Borer (KSHB)  Euwallacea  sp. near  fornicatus .    Results  Hydrogen concentration is a critical signal in fungi for growth and host colonization, the aim of this study was to evaluate the effect of different pH conditions on growth and gene expression of the fungus  Fusarium  sp. associated with KSHB. An RNA-seq approach was used to compare the gene expression of the fungus grown for 2 weeks in liquid medium at three different pH levels (5.0, 6.0, and 7.0). An unbuffered treatment was included to evaluate the capability of the fungus to change the pH of its environment and the impact in gene expression. The results showed that the fungus can grow and modulate its genetic expression at different pH conditions; however, growth was stunted in acidic pH in comparison with neutral pH. The results showed a differential expression pattern in each pH condition even when acidic conditions prevailed at the end of the experiment. After comparing transcriptomics data from the three treatments, we found a total of 4,943 unique transcripts that were differentially expressed.    Conclusions  We identified transcripts related to pH signaling such as the conserved PAL/RIM pathway, some transcripts related to secondary metabolism and other transcripts that were differentially expressed. Our analysis suggests possible mechanisms involved in pathogenicity in this novel  Fusarium  species .  This is the first report that shows transcriptomic data of this pathogen as well as the first report of genes and proteins involved in their metabolism identifying potential virulence factors.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5083-1) contains supplementary material, which is available to authorized users.

Environmental pH modulates transcriptomic responses in the fungus Fusarium sp. associated with KSHB Euwallacea sp. near fornicatus