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Background   Ashbya gossypii  is an industrially relevant microorganism traditionally used for riboflavin production. Despite the high gene homology and gene order conservation comparatively with  Saccharomyces cerevisiae , it presents a lower level of genomic complexity. Its type of growth, placing it among filamentous fungi, questions how close it really is from the budding yeast, namely in terms of metabolism, therefore raising the need for an extensive and thorough study of its entire metabolism. This work reports the first manual enzymatic genome-wide re-annotation of  A. gossypii  as well as the first annotation of membrane transport proteins.    Results  After applying a developed enzymatic re-annotation pipeline, 847 genes were assigned with metabolic functions. Comparatively to KEGG’s annotation, these data corrected the function for 14% of the common genes and increased the information for 52 genes, either completing existing partial EC numbers or adding new ones. Furthermore, 22 unreported enzymatic functions were found, corresponding to a significant increase in the knowledge of the metabolism of this organism. The information retrieved from the metabolic re-annotation and transport annotation was used for a comprehensive analysis of  A. gossypii ’s metabolism in comparison to the one of  S. cerevisiae  (post-WGD – whole genome duplication) and  Kluyveromyces lactis  (pre-WGD), suggesting some relevant differences in several parts of their metabolism, with the majority being found for the metabolism of purines, pyrimidines, nitrogen and lipids. A considerable number of enzymes were found exclusively in  A. gossypii  comparatively with  K. lactis  (90) and  S. cerevisiae  (13). In a similar way, 176 and 123 enzymatic functions were absent on  A. gossypii  comparatively to  K. lactis  and  S. cerevisiae , respectively, confirming some of the well-known phenotypes of this organism.    Conclusions  This high quality metabolic re-annotation, together with the first membrane transporters annotation and the metabolic comparative analysis, represents a new important tool for the study and better understanding of  A. gossypii ’s metabolism.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-810) contains supplementary material, which is available to authorized users.

bmc genomics

Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis