Comparative plastome analyses and phylogenetic insights of Blumea DC

Blumea DC. comprises approximately 100 species with significant morphological diversity. Yet its plastome has rarely been systematically investigated. Previous studies had divided the genus into three main clades: the B. lacera clade, the B. densiflora clade, and the B. balsamifera clade; however, the phylogenetic positions of these clades remain ambiguous. Furthermore, the monophyly of B. formosana, B. sinuata, B. megacephala, B. aromatica, B. axillaris, and B. hieraciifolia is unresolved and requires further investigation. The exact phylogenetic position of Cyathocline Cass., which has been subsumed into Blumea, also remains unclear.

To investigate plastome features in Blumea, plastomes from 23 species and two varieties (including 23 newly sequenced samples and two publicly available representatives) were compared. Comparative analyses assessed structural and sequence variation, divergence hotspots, simple sequence repeats (SSRs), and codon usage bias. Additionally, phylogenetic inference was performed using a dataset of 47 complete plastomes and 38 nrDNA sequences to reconstruct the backbone phylogeny and address the aforementioned phylogenetic problems.

All Blumea plastomes exhibited a typical quadripartite structure with sizes ranging from 150,779 bp to 151,281 bp and contained 113 unique genes (79 protein-coding genes, 30 tRNA genes, and four rRNA genes). IRscope and Mauve analyses revealed minimal structural variation among plastomes. Despite the genes flanking each junction being identical, the junction between LSC, SSC, and IRs regions was classified into four types based on the variations in the distances between genes and their respective junctions. Nine divergent hotspot regions were identified as candidate DNA barcodes for future species identification. Between 79 and 95 SSRs were detected per plastome, predominantly in the large single-copy region and mainly comprising mononucleotide repeats. The genus displayed mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide repeats, with specific types and quantities varying among species. Codon usage bias analysis indicated conservation in preferred codon types, numbers, and RSCU values. Phylogenetic analyses consistently supported the division of Blumea into four clades: the B. lacera clade, B. balsamifera clade, B. densiflora clade, and B. stricta clade. Besides, the monophyly of B. formosana, B. sinuata, B. aromatica, and B. hieraciifolia was well supported.

This study conducts the first large-scale comparative analysis of Blumea plastomes to date, systematically revealing the conservation and specificity of plastome features of the genus. Phylogeny based on plastome and nrDNA dataset has provided an enhanced phylogenetic framework, and preliminary clarified the phylogeny of the genus. Moreover, the monophyly of taxa including B. formosana, B. sinuata, B. megacephala, B. aromatica, B. axillaris, and B. hieraciifolia was well examined. In summary, this study provided substantial informative genetic data pertinent to Blumea and offered new insights into the phylogeny of Blumea, laying the foundation for subsequent taxonomic, systematic, and identification studies.