Comparative chloroplast genome analyses provide new insights into phylogeny of Taraxacum and molecular markers for distinguishing rubber producing dandelions from their weedy relatives in China

Taraxacum species are utilized as traditional herbal medicine or as industrial crops to producing natural rubber. However, the classification of Taraxacum species has long been a challenge, thereby limiting their industrial application. To facilitate the correct screening rubber-producing dandelions from the weedy relatives, 38 chloroplast (Cp) genomes of Taraxacum spp. mainly gathered in Xinjiang, China, were assembled, including both rubber- and non-rubber-producing ones, and were used to reconstruct the phylogeny of Taraxacum. The results reveal that T. mongolicum and T. dealbatum are the primitive species in Taraxacum studied here, while T. erythrospermum and T. compactum are the closest relatives to the rubber-producing dandelion T. kok-saghyz. The discrepancies among the phylogenetic relationships inferred from Cp genomes, nuclear ribosomal internal transcribed spacer and morphology traits reflect chloroplast capture events due to putative ancient cross-species hybridization within Taraxacum. Comparative genomic analysis showed that, although highly conserved for most areas, some regions exhibit relatively high levels of variation in Cp genomes among different Taraxacum species, such as ndhD-ccsA and trnL-trnF regions. A total of 37 loci in Taraxacum Cp genomes were identified as novel putative molecular markers that might assist to distinguish rubber producing dandelions from their weedy relatives in their distribution center. Our results provide new insights into the phylogenetic relationships within the genus Taraxacum. In addition, the Cp genomic resources reported in this study provide genetic foundation for distinguishing rubber producing dandelions from their weedy relatives and future exploration of these industrial important species.