The dried roots of the perennial herb Angelica sinensis (Oliv.) Diels (AS) are commonly used as medicinal and edible resources. In commercial planting, early bolting and flowering (EB) of ca. 60% in the medicine formation period reduces root yield and quality, becoming a significant bottleneck in agricultural production. In the cultivation process, summer bolting (SB) occurs from June to July, and autumn bolting (AB) occurs in September. The AB root is often mistaken for the AS root due to its similar morphological characteristics. Few studies have involved whether the root of AB could be used as herbal medicine. This study explored and compared the accumulation dynamics of primary and secondary metabolites in AS and EB roots during the vegetative growth stage (from May to September) by light microscopy, ultraviolet spectrometry, and HPLC methods. Under a microscope, the amount of free starch granules and oil chamber in the AS root increased. On the contrary, they decreased further from EB-Jul to EB-Sep. By comparison, the wall of the xylem vessel was slightly thickened and stacked, and the cell walls of parenchyma and root cortex tissue were thickened in the EB root. Early underground bolting reduces soluble sugar, soluble protein, free amino acids, total C element, total N element, ferulic acid, and ligustilide accumulation, accompanied by the lignification of the root during the vegetative growth stage. Furthermore, a total of 55 root samples from different bolting types of AS root (29 samples), SB root (14 samples), and AB root (12 samples) were collected from Gansu Province during the harvesting period (October). The later the bolting occurred, the less difference there was between unbolted and bolted roots in terms of morphological appearance and efficacy components. Fourier transform infrared spectroscopy with the attenuated total reflection mode (ATR-FTIR) provides a “holistic” spectroscopic fingerprinting of all compositions in the tested sample. The ATR-FTIR spectrum of the AB root was similar to that of the AS root. However, the number and location of absorption peaks in the spectra of SB were different, and only one strong absorption peak at 1021 cm⁻¹ was regarded as the characteristic peak of C-O stretching vibration in lignin. The ATR-FTIR spectra can be effectively differentiated based on their various characteristics using orthogonal partial least squares discrimination analysis (OPLS-DA). Results were assessed using multiple statistical techniques, including Spearman’s correlation, principal component analysis (PCA), partial least squares discriminant analysis (PLS-DA), and OPLS-DA. Among these methods, the ATR-FTIR data demonstrated the most effective outcomes in differentiating between viable and non-viable roots for their application in herbal medicine. Essential substances are ferulic acid and flavonoid, which are much more abundant in the AB root. It provides a material basis for the pharmacological action of the AB roots and a theoretical basis for improving their availability.

Pyrola decorata Andres (P. decorata) is a traditional medicinal plant in China. However, its chloroplast genome and the deep evolutionary relationships among its genus remain unexplored. This study identified the samples as P. decorata using morphological observations from Flora of China (FOC) and ITS sequences. It is the first to analyze the complete chloroplast genome of P. decorata using Illumina and Nanopore sequencing technologies, confirming a typical chloroplast dumbbell structure. The chloroplast DNA (cpDNA) of P. decorata is 179,999 bp in length, consisting of a large single copy (LSC) (62.3% of total length (112,150 bp)), a small single copy (SSC) (6.5% of total length (11,701 bp)), and two inverted repeat regions (IRA and IRB) (31.2% combined (28,074 bp × 2)). Functional annotation revealed 128 genes: 77 conserved coding sequences (CDS) genes, 43 transfer RNA (tRNA) genes, and 8 ribosomal RNA (rRNA) genes. Phylogenetic analysis placed P. decorata, Pyrola atropurpurea (P. atropurpurea), Pyrola rotundifolia (P. rotundifolia), and Chimaphila japonica within Group I, with P. decorata exhibiting the closest chloroplast genomic affinity to P. atropurpurea. These findings integrate morphological and molecular evidence to facilitate further identification, classification, and evolutionary analysis of this genus.

Armillaria species hold significant ecological and economic importance and they play a vital role in the growth of traditional Chinese medicine Gastrodia elata (G. elata). In this study, we assembled and compared the mitochondrial genomes (mitogenomes) of six Armillaria mellea (Vahl) P. Kumm. (A. mellea) strains isolated from the main G. elata-producing region of Hanzhong, China. The internal transcribed spacer (ITS) sequencing confirmed that all six strains form a monophyletic clade. Their mitogenomes (120,775 to 120,839 bp) exhibit a highly conserved architecture, each containing 16 protein-coding genes (PCGs), 23 open reading frames (ORFs), 27 tRNAs, and two rRNAs. Codon usage and amino acid frequency were strikingly similar among the six strains, with a strong AT bias. In contrast, comparisons with other Armillaria species revealed marked differences in gene order, repeat structures, and selection pressures. Phylogenetic analyses based on PCGs further resolved the close relationship among the six strains while highlighting distinct molecular variation across species. On the whole, these findings demonstrate that A. mellea strains co-evolving with G. elata maintain a highly uniform mitochondrial genome architecture, suggesting strong purifying selection or recent divergence within this symbiotic population. The pronounced differences from other Armillaria species at the levels of gene arrangement and selection pressure imply that mitochondrial gene rearrangement may have accompanied species diversification in the genus. By providing the first complete mitogenomes of A. mellea from a major G. elata cultivation area, this study not only expands the genomic resources for Armillaria but also establishes a foundation for understanding how mitochondrial variation might influence fungal growth, adaptation, and symbiotic efficiency with G. elata.