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Background  Ionic liquids (ILs) draw attention as green solvents for pretreatment of lignocellulose before enzymatic saccharification. Imidazolium-based ILs with different anionic constituents ([HSO 4 ] − , [Cl] − , [MeCO 2 ] − ) were compared with regard to pretreatment of wood from aspen and spruce. The objective was to elucidate how the choice of anionic constituent affected the suitability of using the IL for pretreatment of hardwood, such as aspen, and softwood, such as spruce. The investigation covered a thorough analysis of the mass balance of the IL pretreatments, the effects of pretreatment on the cell wall structure as assessed by fluorescence microscopy, and the effects of pretreatment on the susceptibility to enzymatic saccharification. Torrefied aspen and spruce were included in the comparison for assessing how shifting contents of hemicelluloses and Klason lignin affected the susceptibility of the wood to IL pretreatment and enzymatic saccharification.    Results  The glucose yield after IL pretreatment increased in the order [Cl] −  < [HSO 4 ] −  < [MeCO 2 ] −  for aspen, but in the order [HSO 4 ] −  < [Cl] −  < [MeCO 2 ] −  for spruce. For both aspen and spruce, removal of hemicelluloses and lignin increased in the order [Cl] −  < [MeCO 2 ] −  < [HSO 4 ] − . Fluorescence microscopy indicated increasingly disordered cell wall structure following the order [HSO 4 ] −  < [Cl] −  < [MeCO 2 ] − . Torrefaction of aspen converted xylan to pseudo-lignin and changed the glucose yield order to [HSO 4 ] −  < [Cl] −  < [MeCO 2 ] − .    Conclusions  The acidity of [HSO 4 ] −  caused extensive hydrolysis of xylan, which facilitated pretreatment of xylan-rich hardwood. Apart from that, the degree of removal of hemicelluloses and lignin did not correspond well with the improvement of the enzymatic saccharification. Taken together, the saccharification results were found to mainly reflect ( i ) the different capacities of the ILs to disorder the cell wall structure, ( ii ) the recalcitrance caused by high xylan content, and ( iii ) the capacity of the [HSO 4 ] − -based IL to hydrolyze xylan.    Electronic supplementary material  The online version of this article (10.1186/s12896-017-0403-0) contains supplementary material, which is available to authorized users.

Comparison of [HSO4]−, [Cl]− and [MeCO2]− as anions in pretreatment of aspen and spruce with imidazolium-based ionic liquids