Complete chloroplast genome data reveal the existence of the Solidago canadensis L. complex and its potential introduction pathways into China

<i>Solidago canadensis</i>, native to North America, is an invasive species in many areas of the world, where it causes serious damage to natural ecosystems and economic losses. However, a dearth of genetic resources and molecular markers has hampered our understanding of its invasion history. Here, we <i>de novo</i> assembled 40 complete chloroplast genomes of <i>Solidago</i> species, including 21 <i>S. canadensis</i> individuals, 15 <i>S. altissima</i> individuals, and four <i>S. decurrens</i> individuals, the sizes of which ranged from 152,412 bp to 153,170 bp. The phylogenetic trees based on the complete chloroplast genome sequences and nuclear genome-wide SNP data showed that <i>S. canadensis</i> and <i>S. altissima</i> cluster together and form a monophyletic pair, as sister to <i>S. decurrens</i>, indicating the existence of the <i>S. canadensis</i> L. complex in China. Three potential introduction pathways were identified. The chloroplast-genome structure and gene contents are conservative in the genomes of the <i>S. canadensis</i> L. complex and <i>S. decurrens</i>. The analysis of sequence divergence indicated five variable regions, and 10 chloroplast protein-coding genes that underwent positive selection were identified. Our findings shed new light on the invasion history of <i>S. canadensis</i> and the data sets generated in this study will facilitate future research on its chloroplast genome evolution.