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Background   Mikania micrantha  H.B.K. (Asteraceae) is one of the world’s most invasive weeds which has been rapidly expanding in tropical Asia, including China, while its close relative  M. cordata , the only  Mikania  species native to China, shows no harm to the local ecosystems. These two species are very similar in morphology but differ remarkably in several ecological and physiological traits, representing an ideal system for comparative analysis to investigate the genetic basis underlying invasion success. In this study, we performed RNA-sequencing on the invader  M. micrantha  and its native congener  M. cordata  in China, to unravel the genetic basis underlying the strong invasiveness of  M. micrantha . For a more robust comparison, another non-invasive congener  M. cordifolia  was also sequenced and compared.    Results  A total of 52,179, 55,835, and 52,983 unigenes were obtained for  M. micrantha ,  M. cordata , and  M. cordifolia , respectively. Phylogenetic analyses and divergence time dating revealed a relatively recent split between  M. micrantha  and  M. cordata , i.e., approximately 4.81 million years ago (MYA), after their divergence with  M. cordifolia  (8.70 MYA). Gene ontology classifications, pathway assignments and differential expression analysis revealed higher representation or significant up-regulation of genes associated with photosynthesis, energy metabolism, protein modification and stress response in  M. micrantha  than in  M. cordata  or  M. cordifolia . Analysis of accelerated evolution and positive selection also suggested the importance of these related genes and processes to the adaptability and invasiveness of  M. micrantha . Particularly, most (77 out of 112, i.e. 68.75%) positively selected genes found in  M. micrantha  could be classified into four groups, i.e., energy acquisition and utilization (10 genes), growth and reproduction (13 genes), protection and repair (34 genes), and signal transduction and expression regulation (20 genes), which may have contributed to the high adaptability of  M. micrantha  to various new environments and the capability to occupy a wider niche, reflected in its high invasiveness.    Conclusions  We characterized the transcriptomes of the invasive species  M. micrantha  and its non-invasive congeners,  M. cordata  and  M. cordifolia . A comparison of their transcriptomes provided insights into the genetic basis of the high invasiveness of  M. micrantha .    Electronic supplementary material  The online version of this article (10.1186/s12864-018-4784-9) contains supplementary material, which is available to authorized users.

bmc genomics

Comparative transcriptome analysis of the invasive weed Mikania micrantha with its native congeners provides insights into genetic basis underlying successful invasion