Mitochondria regulate nuclear genomes and their own genetic material, primarily to provide energy in eukaryotes. Currently, high-throughput sequencing technologies are being used to resolve the mitochondrial genomes of various edible fungi. However, the application of pan-genomes for the analysis of edible mushroom mitochondrial genomes remains unexplored. In this study, we conducted a comparative mitochondrial genome analysis of 31 Hypsizygus marmoreus strains (four newly sequenced monotypes and 27 public datasets), ranging from 98,284 to 111,087 bp. This variation was determined to be primarily driven by dynamic changes in non-coding regions, particularly intronic polymorphisms in the cox1 gene. Further, transfer RNA (tRNA) secondary structures exhibited atypical globular and elongated conformations alongside copy number variations. Additionally, codon usage showed a pronounced A/T bias, whereas core respiratory chain genes demonstrated an evolutionary pattern of strong purifying selection. Furthermore, the 31 mitochondrial genomes of H. marmoreus were found to harbor eight gene rearrangement patterns and five genetic clusters, and the pan-genome analysis (220,364 bp, 217 nodes) captured abundant single-nucleotide polymorphisms (SNPs), insertions/deletions (InDels), and structural variations. This study provides breeding-relevant genetic markers and a genomic framework for H. marmoreus germplasm classification, genetic improvements, and the molecular breeding of stress-resilient varieties.

Light-harvesting chlorophyll a/b-binding (Lhc) proteins are integral membrane proteins that bind to pigment molecules, playing a critical role in photosynthetic processes, including light energy harvesting and transfer. To investigate the role of the Lhc gene family in cucumber (Cucumis sativus L), genome-wide identification of CsLhc gene family members and analysis of their regulatory networks were carried out using bioinformation and molecular biology research methods at Anhui Science and Technology University. The results indicated that the Lhc family consisted of 21 members, being categorized into five subfamilies: Lhca, Lhcb, CP24, CP26, and CP29. The gene structure and motifs within each subfamily are generally conserved. CsLhcs are distributed on seven chromosomes, including one pair of tandem duplicates and two pairs of segmental duplicates. Six CsLhcs exhibit eight linear relationships with seven AtLhcs, and one CsLhc shows a syntenic relationship with one OsLhc. Analysis of the cis-acting elements in CsLhc promoters revealed their potential involvement in stress responses. Transcriptome data indicated that CsLhcs are minimally expressed in male flowers and roots, but highly expressed in other organs. Analysis of stress response processes revealed that all Lhc genes participate in at least one stress response. Five Lhc genes were confirmed to appear to have expression change using qPCR analysis under high temperature and salt stress. Particularly, under downy mildew, root-knot nematode stresses, and blight stress, up-regulated Lhc genes were the most abundant ones, indicating that the Lhc family acts as a significant role in the growth and development of cucumber. These results provide valuable insights for further understanding the characteristics of the CsLhc family and analyzing the function of the Lhc family in cucumber resistance to biotic/abiotic stresses and in molecular breeding.

Exogenous nutrient bags are essential for the artificial cultivation of Morchella sextelata, but the effects of different formulations on yield, nutritional quality, and the soil microecological environment remain unclear. In this study, nine exogenous nutrient bag formulations and one conventional treatment (CK) were evaluated during M. sextelata cultivation. Fruiting time, fresh and dry yields, and nutritional quality indicators were measured, and principal component analysis combined with membership function analysis was used for comprehensive evaluation. Soil physicochemical properties were determined for all treatments, and A7, A3, and CK were selected to represent the best-performing, worst-performing, and conventional treatments, respectively, for soil microbial community analysis. Different formulations significantly affected agronomic and nutritional traits (p < 0.01). A6 showed the shortest fruiting time and the highest fresh and dry yields, whereas A7 had the highest polysaccharide content and ranked first in the comprehensive evaluation. The D values of A7, A6, and CK were 0.789, 0.777, and 0.653, respectively. Soil nutrient analysis showed that morel cultivation markedly altered soil nutrient structure, especially available nutrients and phosphorus-related indicators. Microbial analysis showed that A7 had the highest bacterial richness among the three sequenced treatments and stronger colonization by M. sextelata. Its bacterial and fungal communities were also more closely associated with soil organic carbon. Overall, A6 was more suitable for yield-oriented production, whereas A7 showed the best comprehensive performance when yield, nutritional quality, and soil ecological characteristics were considered together.