Dioscorea alata L. (Dioscoreaceae), commonly known as greater yam, water yam, or winged yam, is a popular tuber vegetable/food crop worldwide, with nutritional, health, and economical importance. China is an important domestication center of D. alata, and hundreds of cultivars (accessions) have been established. However, genetic variations among Chinese accessions remain ambiguous, and genomic resources currently available for the molecular breeding of this species in China are very scarce. In this study, we generated the first pan-plastome of D. alata, based on 44 Chinese accessions and 8 African accessions, and investigated the genetic variations, plastome evolution, and phylogenetic relationships within D. alata and among members of the section Enantiophyllum. The D. alata pan-plastome encoded 113 unique genes and ranged in size from 153,114 to 153,161 bp. A total of four whole-plastome haplotypes (Haps I–IV) were identified in the Chinese accessions, showing no geographical differentiation, while all eight African accessions shared the same whole-plastome haplotype (Hap I). Comparative genomic analyses revealed that all four whole plastome haplotypes harbored identical GC content, gene content, gene order, and IR/SC boundary structures, which were also highly congruent with other species of Enantiophyllum. In addition, four highly divergent regions, i.e., trnC–petN, trnL–rpl32, ndhD–ccsA, and exon 3 of clpP, were identified as potential DNA barcodes. Phylogenetic analyses clearly separated all the D. alata accessions into four distinct clades corresponding to the four haplotypes, and strongly supported that D. alata was more closely related to D. brevipetiolata and D. glabra than D. cirrhosa, D. japonica, and D. polystachya. Overall, these results not only revealed the genetic variations among Chinese D. alata accessions, but also provided the necessary groundwork for molecular-assisted breeding and industrial utilization of this species.

Pyracantha fortuneana (Maxim.) Li (Rosaceae), commonly known as Chinese firethorn, is an evergreen shrub with high nutritional, medicinal, and horticultural importance. This species typically has white flowers, but a rare red flower phenotype has been found in very few wild populations in western Hubei, China, showing great ornamental potential. In this study, the complete chloroplast genome of the red flower phenotype of P. fortuneana was reported for the first time, using high-throughput sequencing technology. The complete chloroplast genome was 160,361 bp in length and showed a typical quadripartite structure with a pair of inverted repeat (IR) regions (26,350 bp) separated by a large single-copy (LSC) region (88,316 bp) and a small single-copy (SSC) region (19,345 bp). A total of 131 functional genes were annotated in this chloroplast genome, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. Comparative chloroplast genome analyses revealed that high genome similarity existed not only between red and white flower phenotypes of P. fortuneana, but also among Pyracantha species. No evidence for positive selection was found in any PCG, suggesting the evolutionary conservation of Pyracantha chloroplast genomes. Furthermore, four mutational hotspots (trnG-trnR-atpA, psbZ-trnG-trnfM-rps14, ycf3-trnS-rps4, and ndhF-rpl32) with π > 0.004 were identified as potential molecular markers for Pyracantha species. Phylogenomic analysis strongly supported that the red flower phenotype of P. fortuneana was nested within the common white flower phenotype. Based on both morphological and molecular evidence, we suggest that the red flower phenotype of P. fortuneana could be considered as a new forma. Overall, the availability of these genetic resources will not only offer valuable information for further studies on molecular taxonomy, phylogeny, and population genetics of Pyracantha species but also could be used as potential genetic resources for Chinese firethorn breeding.

The greater yam (Dioscorea alata), a widely cultivated and nutritious food crop, suffers from widespread yield reduction due to anthracnose caused by Colletotrichum gloeosporioides. Latent infection often occurs before anthracnose phenotypes can be detected, making early prevention difficult and causing significant harm to agricultural production. Through comparative genomic analysis of 60 genomes of 38 species from the Colletotrichum genus, this study identified 17 orthologous gene groups (orthogroups) that were shared by all investigated C. gloeosporioides strains but absent from all other Colletotrichum species. Four of the 17 C. gloeosporioides-specific orthogroups were used as molecular markers for PCR primer designation and C. gloeosporioides detection. All of them can specifically detect C. gloeosporioides out of microbes within and beyond the Colletotrichum genus with different sensitivities. To establish a rapid, portable, and operable anthracnose diagnostic method suitable for field use, specific recombinase polymerase amplification (RPA) primer probe combinations were designed, and a lateral flow (LF)-RPA detection kit for C. gloeosporioides was developed, with the sensitivity reaching the picogram (pg) level. In conclusion, this study identified C. gloeosporioides-specific molecular markers and developed an efficient method for C. gloeosporioides detection, which can be applied to the prevention and control of yam anthracnose as well as anthracnose caused by C. gloeosporioides in other crops. The strategy adopted by this study also serves as a reference for the identification of molecular markers and diagnosis of other plant pathogens.

Background/Objectives: Changnienia amoena is a rare and endangered terrestrial orchid endemic to China, valued for its ornamental and medicinal properties. However, limited genomic resources hinder its effective conservation strategies and sustainable utilization. This study aimed to generate comprehensive plastome resources and develop molecular markers to support the phylogenetics, identification, and conservation management of C. amoena. Methods: Genome skimming was employed to assemble and annotate the complete plastomes of seven geographically distinct C. amoena accessions. Comparative analyses were conducted to assess structural features and sequence divergence within C. amoena and across related species in the Calypsoinae subtribe. Phylogenetic relationships were inferred from protein-coding genes. Simple sequence repeats (SSRs), dispersed repeats, and hypervariable regions were identified from the plastomes, while nuclear SSRs were developed from assembled nuclear sequences. Results: All seven plastomes exhibited a conserved quadripartite structure with identical gene content and order, showing only minor variations in genome size. Sequence divergence was mainly confined to non-coding regions. Across Calypsoinae species, mycoheterotrophic taxa exhibited reduced plastomes. Phylogenetic analyses resolved four well-supported intergeneric clades within Calypsoinae and revealed a notable divergence between the HuNGZ accession and other C. amoena accessions, which otherwise showed low plastome-level differentiation. We also identified 69–74 plastome-derived SSRs, 22–25 dispersed repeats, and three hypervariable regions that may serve as informative molecular markers for C. amoena. Additionally, 16 polymorphic nuclear SSRs were developed from assembled nuclear sequences. Conclusions: These findings significantly expand the genomic resources available for C. amoena and provide essential insights for its phylogeny, molecular identification, conservation management, and future breeding efforts.

NaOH solutions with different concentration were used to pre-treat YPs (yellow pigments) in order to investigate surface modification effects on stability and particle size of pre-treated yellow pigments (PYPs). The coupling agent KH550 was used to treat PYP10 (yellow pigment pre-treated with 10% NaOH) to be compared for PYPs. The YPs (yellow pigments) were pre-treated by NaOH solutions and rinsed with C2H5OH, then the filtrates and residues were analysed by spectrophotometer and laser granularity analyser; The filtrates are stratified after the PYPs rinsed with C2H5OH. Microscope and Natural settling experiment were used to analyse the particle size and stability in residues. The results show that the particle size of wet PYPs decreased with the concentration of NaOH, and the particle size of PYP30 was smaller than that of PYP10-KH550 (PYP10 treated with 5% KH550). The laser granularity analyser results show that the particle size of dry PYPs increased with the concentration of NaOH. The settle time of PYPs in water indicated that the stability of PYPs increased with the concentration of NaOH and PYP10-KH550 has the poorest stability. These results indicated that PYP30 has smallest particles and best stability, and it has the potential to be used in industry.

SUMMARY: Whole‐genome duplication (WGD, or polyploidization) is a major evolutionary force in plants, yet the genomic, transcriptional, and metabolic consequences of autopolyploidy remain less understood than those of allopolyploidy. Dioscorea nipponica , a medicinal species producing diosgenin‐type steroidal saponins, harbors both diploid and autopolyploid populations, providing a unique system to investigate these processes. Here, we present a haplotype‐resolved, chromosome‐scale genome assembly of autotetraploid D. nipponica (2 n = 4 x = 40). Comparative and population genomic analyses indicate a single, recent autotetraploid origin (<1.63 Ma), after the divergence of its diploid ancestors (~2.5–2.9 Ma), coinciding with Pliocene–Pleistocene climatic shifts that may have promoted population isolation and genome duplication. The four haplotypes exhibit high average nucleotide identity, extensive synteny and similar global gene expression, with pervasive allele loss (~32% of genes) and widespread allelic transcriptional suppression (~60% of expressed tetrads), together buffering dosage effects. Metabolomic profiling reveals a metabolic trade‐off in rhizomes, with autotetraploids accumulating higher flavonoids but lower diosgenin‐type steroidal saponins than diploids, potentially enhancing reproductive fitness and adaptation to marginal environments. This shift is supported by expanded flavonoid gene families (e.g., PAL, CHS), some exhibiting positive dosage effects, whereas diosgenin pathway genes (e.g., CYP90, CYP94) remain copy number stable and mostly show negative dosage effects in autotetraploids. Selective sweep analysis further identified genes linked to genome stability (e.g., AtTOP3α , AtDMC1 ) and abiotic stress response, crucial for polyploid establishment. Overall, these findings offer novel insights into how autopolyploidy shapes gene expression, metabolic evolution, and ecological adaptation, with implications for the conservation and utilization of this medicinally important species.