DNA barcoding and metabolite profiling reveal taxonomic and phytochemical diversity in Sonchus spp.

Abstract

Abstract Accurate species identification is fundamental to biodiversity studies, conservation, and the utilization of medicinal plants. The genusSonchus(Asteraceae) presents significant taxonomic challenges due to morphological plasticity and potential hybridization. DNA barcoding using the chloroplastrbcLand nuclear ribosomal ITS2 regions was used to delimit threeSonchusspecies (S. arvensis,S. oleraceus, andS. malayanus) collected from Bromo Mountain, Indonesia. To complement molecular data and explore chemotaxonomic markers, leaf metabolite profiles were analyzed using gas chromatography-mass spectrometry (GC-MS). TherbcLmarker showed high sequence conservation (99.58-100% identity) across species, confirming genus-level identification but failing to resolve species boundaries. The ITS2 region exhibited moderate variation (98.03-100% identity), with substantial overlap amongS. asper,S. oleraceus, andS. malayanus, suggesting recent divergence or possible conspecificity. Neighbor-joining phylogenetic analysis of both markers clustered accessions into broad clades corresponding to continental and island lineages, though low intraspecific divergence obscured taxonomic resolution. In contrast, GC-MS profiling revealed distinct species-specific chemotypes.Sonchus arvensiswas characterized by high abundances of neophytadiene (27.46%) and phytol (13.22%).Sonchus oleraceuscontained phytol (23.28%) as the major compound, with lower levels of neophytadiene (6.59%) and several methylated fatty acid esters.Sonchus malayanusdisplayed a distinct profile dominated by compounds with lower identification confidence, including (E)-4-trimethylsilyl-3-buten-2-ol (19.21%), alongside confidently identified guaiacol and trimethylamine. The discordance between molecular and chemical data underscores the limitations of single-locus barcoding in closely relatedSonchusspecies. This study demonstrates that integrative taxonomy, combining molecular, phytochemical, and morphological evidence, provides a more robust framework for species delimitation in this genus. The identified volatile compounds, particularly neophytadiene and phytol, represent promising chemotaxonomic markers and warrant further investigation for their ecological and pharmacological significance.