Genomic insights on <i>Mikania micrantha</i> invasiveness: gene family expansion, transposable elements, gene expression, and population structure

Mikania micrantha is an aggressive climbing vine that poses significant threats to ecosystems and causes severe agricultural and economic losses. However, the molecular mechanisms underlying its adaptive evolution and invasion dynamics remain unclear. Comprehensive genomics and resequencing analyses were conducted to unravel the factors driving the adaptive evolution and invasion dynamics of M. micrantha. We confirmed the chromosome number of M. micrantha as 2n = 2x = 36 and generated chromosome-scale genomes for M. micrantha (1.53 Gb) and its native congener M. cordata (1.68 Gb). Comparative genomics identifies three key differences in M. micrantha compared to its native congener: the expansion of growth/defense gene families, transposon-mediated genomic diversity, and stress-related paralog expression plasticity. Whole-genome resequencing revealed high genomic similarity across southern China due to multiple introductions and introgression. Regulatory plasticity in the auxin signaling pathway (miR167a-ARF8) might provide a competitive advantage for M. micrantha. Mikania micrantha exhibited a higher copy number and expression of benzoxazinoids biosynthesis-related genes compared to M. cordata, potentially enhancing its defensive capabilities. This study provides new genomic insights into the invasive success of M. micrantha and suggests that targeting the auxin signaling pathway may offer a promising strategy for controlling the spread of this invasive weed.