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Background  The product yield and titers of biological processes involving the conversion of biomass to desirable chemicals can be limited by environmental stresses encountered by the microbial hosts used for the bioconversion. One of these main stresses is growth inhibition due to exposure to low pH conditions. In order to circumvent this problem, understanding the biological mechanisms involved in acid stress response and tolerance is essential. Characterisation of wild yeasts that have a natural ability to resist such harsh conditions will pave the way to understand the biological basis underlying acid stress resistance.  Pichia anomala  possesses a unique ability to adapt to and tolerate a number of environmental stresses particularly low pH stress giving it the advantage to outcompete other microorganisms under such conditions. However, the genetic basis of this resistance has not been previously studied.    Results  To this end, we isolated an acid resistant strain of  P. anomala , performed a gross phenotypic characterisation at low pH and also performed a whole genome and total RNA sequencing. By integrating the RNA-seq data with the genome sequencing data, we found that several genes associated with different biological processes including proton efflux, the electron transfer chain and oxidative phosphorylation were highly expressed in  P. anomala  cells grown in low pH media. We therefore present data supporting the notion that a high expression of proton pumps in the plasma membrane coupled with an increase in mitochondrial ATP production enables the high level of acid stress tolerance of  P. anomala .    Conclusions  Our findings provide insight into the molecular and genetic basis of low pH tolerance in  P. anomala  which was previously unknown. Ultimately, this is a step towards developing non-conventional yeasts such as  P. anomala  for the production of industrially relevant chemicals under low pH conditions.    Electronic supplementary material  The online version of this article (doi:10.1186/s12934-015-0331-4) contains supplementary material, which is available to authorized users.

RNA-seq analysis of Pichia anomala reveals important mechanisms required for survival at low pH