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Background  Water chickweed ( Myosoton aquaticum  (L.)) is a dicot broadleaf weed that is widespread in winter fields in China, and has evolved serious resistance to acetolactate synthase (ALS) inhibiting herbicides.    Results  We identified a  M. aquaticum  population exhibiting moderate (6.15-fold) resistance to tribenuron-methyl (TM). Target-site ALS gene sequencing revealed no known resistance mutations in these plants, and the in vitro ALS activity assays showed no differences in enzyme sensitivity between susceptible and resistant populations; however, resistance was reversed by pretreatment with the cytochrome P450 (CYP) monooxygenase inhibitor malathion. An RNA sequencing transcriptome analysis was performed to identify candidate genes involved in metabolic resistance, and the unigenes obtained by de novo transcriptome assembly were annotated across seven databases. In total, 34 differentially expressed genes selected by digital gene expression analysis were validated by quantitative real-time (qRT)-PCR. Ten consistently overexpressed contigs, including four for CYP, four for ATP-binding cassette (ABC) transporter, and two for peroxidase were further validated by qRT-PCR using additional plants from resistant and susceptible populations. Three CYP genes (with homology to  CYP734A1 ,  CYP76C1 , and  CYP86B1 ) and one ABC transporter gene (with homology to  ABCC10 ) were highly expressed in all resistant plants.    Conclusion  The mechanism of TM resistance in  M. aquaticum  is controlled by NTSR rather than TSR. Four genes,  CYP734A1 ,  CYP76C1 ,  CYP86B1 , and  ABCC10  could play essential role in metabolic resistance to TM and justify further functional studies. To our knowledge, this is the first large-scale transcriptome analysis of genes associated with NTSR in  M. aquaticum  using the Illumina platform. Our data provide resource for  M. aquaticum  biology, and will facilitate the study of herbicide resistance mechanism at the molecular level in this species as well as in other weeds.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1451-x) contains supplementary material, which is available to authorized users.

Non-target site-based resistance to tribenuron-methyl and essential involved genes in Myosoton aquaticum (L.)