Pear aroma quality is predominantly governed by volatile organic compounds (VOCs), which are critically influenced by postharvest storage conditions. This study tracked VOCs, soluble solids content (SSC), and texture dynamics in Nanguoli, Jingbaili, and Korla pears during 105-day cold storage and a 15-day shelf life. A total of 301 VOCs were identified, with esters increasing dramatically (25.96- to 113.55-fold) after 75-day cold storage, especially in soft-fleshed cultivars. Texture declined in these cultivars during shelf life, whereas Korla pears maintained exceptional firmness (> 90% retention) and stable texture parameters. Multivariate analysis revealed a strong negative correlation (r < -0.8) between ester accumulation and textural integrity, highlighting a fundamental trade-off between tissue softening and aroma development. Furthermore, up to 85 VOCs were identified with variable importance in projection scores > 1. These compounds may help clarify the mechanistic basis of texture deterioration and inform strategies for postharvest quality preservation in future studies.

Wild pear resources are rich in phenolic metabolites and few studies have explored molecular mechanisms underlying polyphenol metabolism in wild pear fruit after storage. In this study, we analyzed changes in total phenolic content, total flavonoid content, antioxidant capacity, phenolic metabolites, and gene expression patterns in wild pear after storage. The results showed that both total phenols and total flavonoids increased after storage, accompanied by enhanced antioxidant capacity. Almost all differentially accumulated phenolic acids and flavonoids were upregulated, whereas almost all lignan-related metabolites were downregulated. Phenylalanine ammonia-lyase (PAL) and p-hydroxycinnamoyl-CoA (HCT) participated in the synthesis of phenolic acids, flavonoids, lignans, and coumarins; shikimate dehydrogenase (SKDH) and chorismate mutase (CM) contributed to phenolic acid formation; dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS) were associated with flavonoid biosynthesis; and dirigent protein (DIR) and β-glucosidase (BGLU) were implicated in lignan and coumarin production. Furthermore, we constructed ceRNA networks related to polyphenol metabolism, correlation networks between differentially expressed genes and metabolites, and metabolic pathways for phenolic acids, flavonoids, lignans, and coumarins. This study clarified variation patterns of polyphenols in wild pear germplasm after storage and might facilitate the breeding of polyphenol pear varieties.

Climate change is profoundly affecting global ecosystems and biodiversity, with fruit trees being one of the plant groups relatively sensitive to climate change. China is one of the centers of diversity for the genus Pyrus, harboring abundant wild and cultivated germplasm resources. However, systematic assessments of the responses of Pyrus species to future climate change at the national scale in China using species distribution modelling remain limited. In this study, we compiled 153 occurrence records of Pyrus betulifolia, 47 of Pyrus pyrifolia, and 117 of Pyrus ussuriensis, and integrated climatic, soil, topographic, and anthropogenic variables. A biomod2-based ensemble modelling framework was used to predict potential suitable habitats under current and future climate scenarios and to identify key environmental drivers. The results showed that temperature seasonality (Bio4) was the dominant factor influencing the distributions of P. betulifolia and P. ussuriensis, whereas precipitation of the warmest quarter (Bio18) was the primary driver of P. pyrifolia. Under current climatic conditions, highly suitable habitats accounted for 4.04

Pear (Pyrus L.) is a fruit tree of global commercial importance. Its genetic relationships, evolutionary history, dissemination routes, and genetic determinants of most agronomic traits remain to be elucidated. We conducted whole-genome resequencing of 495 Pyrus accessions. Phylogenetic and demographic analyses resolved geographic groupings of the accessions, identifying the Yunnan-Guizhou Plateau as the putative dissemination center for cultivated Pyrus pyrifolia and P. bretschneideri. Identification of two evolutionary bottlenecks provides insights into the population dynamics of pear species. Admixture and introgression analyses revealed both intraspecific and interspecific genetic exchanges, substantiating the complex emergence of cultivated populations. Genome-wide association study (GWAS) identified loci associated with nine crucial agronomic traits, together with eight candidate genes. The GWAS, molecular, and biochemical analyses suggested that PbeMADS25, PbeSPP, PbeDHQ-SDH, PbeARF2, PbePPO, PbePIN3, PbeCXE, and PbeMYB38 participate in the regulation of number of stigmas and number of locules, number of stamens, young leaf color, sepal persistence, astringency, acidity, aroma, and fruit skin color, respectively. Overexpression and metabonomic analysis of PbeCXE indicated that it affects the fruit aroma by affecting the balance between ester biosynthesis and substrate consumption. These findings expand our understanding of Pyrus evolution and provide a genomic foundation for genetic improvement of agronomic traits.

BACKGROUND:Pear is one of the most popular and widely cultivated fruits globally, with rich cultivar diversity. Pyrus species are characterized by self-incompatibility and the absence of reproductive barriers between species, leading to extensive gene flow and genetic recombination among different types of cultivars. As a result, cultivar identification technologies have considerable practical significance in pear production. Multiple nucleotide polymorphism (MNP) technology, which combines multiplex PCR amplification and high-throughput sequencing, offers high efficiency and accuracy in pear cultivar identification, and meets the needs of cultivar innovation and industry development. RESULTS:We applied MNP technology to pear cultivar identification for the first time, establishing fingerprints for major pear cultivars and exploring the feasibility of MNP markers for pear population structure analysis. Based on genomic resequencing data from 143 pear accessions, 558 marker loci were initially developed, and 310 core markers were retained after screening. The 310 MNP markers showed high polymorphism, with an average of 18.14 alleles per marker locus and PIC values ranging from 0.57 to 0.99. Validation using 76 representative pear cultivars demonstrated reproducibility and accuracy rates exceeding 99% for the 310 MNP markers. A total of 2,850 pairwise comparisons among the 76 cultivars showed an average genetic differentiation of 90.89%. Population structure analyses based on MNP markers effectively reflected the classification relationships among the 76 cultivars, clearly distinguishing European from Asian pears. CONCLUSION:In summary, the developed pear MNP markers possess high polymorphism, stability, and cultivar-discrimination capability, promising extensive future applications in pear cultivar identification and population genetic research.

Introduction:Wild Ussurian Pear germplasm resource has rich genetic diversity, which is the basis for genetic improvement of pear varieties. Accurately and efficiently identifying wild Ussurian Pear accession is a prerequisite for germplasm conservation and utilization. Methods:We proposed YOLOv10n-MCS, an improved model featuring: (1) Mixed Local Channel Attention (MLCA) module for enhanced feature extraction, (2) Simplified Spatial Pyramid Pooling-Fast (SimSPPF) for multi-scale feature capture, and (3) C2f_SCConv backbone to reduce computational redundancy. The model was trained on a self-made dataset of 16,079 wild Ussurian Pear leaves images. Results:Experiment results demonstrate that the precision, recall, mAP50, parameters, FLOPs, and model size of YOLOv10n-MCS reached 97.7(95% CI: 97.18 to 98.16)%, 93.5(95% CI: 92.57 to 94.36)%, 98.8(95% CI: 98.57 to 99.03)%, 2.52M, 8.2G, and 5.4MB, respectively. The precision, recall, and mAP50 are significant improved of 2.9%, 2.3%, and 1.5% respectively over the YOLOv10n model (p<0.05). Comparative experiments confirmed its advantages in precision, model complexity, model size, and other aspects. Discussion:This lightweight model enables real-time wild Ussurian Pear identification in natural environments, providing technical support for germplasm conservation and crop variety identification.

Located in the southwestern region of China, the Yunnan–Kweichow Plateau, is closely related to the origins of Pyrus L. Despite this important status, there has been relatively little population genetics research focused on the wild Pyrus species in this area. To address this gap in knowledge, the present study was conducted investigating wild Pyrus species distributions in the Yunnan–Kweichow Plateau region. These analyses entailed the collection of 80 accessions, whole-genome resequencing, and the detection of variants including SNPs, InDels, SVs, and CNVs. Genetic structure analyses revealed clear differences between P. pashia and P. calleryana, where the former was additionally subdivided into five groups. The genetic structure of these accessions was closely aligned with their geographic distribution, highlighting the fragmented nature of wild Pyrus populations on the Yunnan–Kweichow Plateau. Analyses of genetic diversity suggested that the central and easter portions of Yunnan Province are key centers of Pyrus diversity on the Yunnan–Kweichow Plateau, whereas the highest degree of differentiation was observed for wild Pyrus in the southwest and northwest regions. Demographic analyses indicated that wild Pyrus populations on the Yunnan–Kweichow Plateau are currently in a state of population contraction, with evidence of migration events between these populations.

Understanding complex biological systems requires tracing cellular dynamic changes across conditions, time, and space. However, integrating multi-sample data in a unified way to explore cellular heterogeneity remains challenging. Here, we present Stereopy, a flexible framework for modeling and dissecting comparative and spatiotemporal patterns in multi-sample spatial transcriptomics with interactive data visualization. To optimize this framework, we devise a universal container, a scope controller, and an integrative transformer tailored for multi-sample multimodal data storage, management, and processing. Stereopy showcases three representative applications: investigating specific cell communities and genes responsible for pathological changes, detecting spatiotemporal gene patterns by considering spatial and temporal features, and inferring three-dimensional niche-based cell-gene interaction network that bridges intercellular communications and intracellular regulations. Stereopy serves as both a comprehensive bioinformatics toolbox and an extensible framework that empowers researchers with enhanced data interpretation abilities and new perspectives for mining multi-sample spatial transcriptomics data.

[Objective] Weixian has a long pear cultivation history with approximately 20 unique local pear cultivars, including the most famous Weixian Yali. Researchers have made significant progress in the collection, preservation and phenotypic evaluation on pear germplasm resources in Weixian, but the genetic relationship and background of these pears remain largely unexplored. To provide a theory basis for the efficient utilization of Weixian pears and the sustainable development of pear industry, it is needed to elucidate the genetic relationship and background of Weixian pear accessions. [Methods] Twenty local pear cultivars from Weixian and 10 representative local pear cultivars from other regions within Hebei province were selected as research materials. Based on the whole-genome resequencing data and chloroplast DNA variation, we investigated the genetic relationship and background of local pear cultivars in Weixian. The clean reads were aligned to the reference genome Yunhong No.1 using BWA v0.7.15 software for whole-genome alignment; SNP detection and filtering were performed using GATK v4.2.5.0 software; Population structure analysis was conducted using Admixture v1.3.0 and principal component analysis was carried out using GCTA v1.93.2 software; Treebest v1.9.2 software was used to calculate the distance matrix, and a phylogenetic tree was constructed using the neighbor-joining method. The chloroplast DNA sequencing results were aligned and manually corrected using the software MEGA X; the genetic parameters of chloroplast DNA sequence fragments were calculated using the software DnaSP 5.1; the evolutionary relationship between haplotypes was analyzed using the software NetWork 10. [Results] By comparing the resequencing data of 30 materials with the reference genome, a total of 30 041, 877 SNP loci were identified. We performed principal component analysis, population genetic structure and phylogenetic tree based on these SNPs. The results showed that local pear cultivars in Weixian exhibited a clear population genetic structure, which could be divided into two groups: Group 1 consisted of 9 materials including Weixian Hongli, Youqiu, Xiaohongmian, Baidunzili, Baihongli, Dunzili, Jinfeng Yali, Kaixinmian and Suanjiuli; Group 2 comprised the remaining 11 materials from Weixian, including Xiaobaimian, Xuehua, Wu'an Youqiu, Dabaimian, Yayamian, Teda Baimian, Baixuehua, Yinbai, Yali, Teda Yali, Meixiang Yali and Xiaobaimian, which can be further divided into two subgroups. Additionally, Group 2 included 10 local pear cultivars from northern Hebei, like Anli and Baihuaguan, indicating a close genetic relationship between Weixian pears in Group 2 and northern pear cultivars. In contrast, Weixian Hongli in Group 1 belonged to the Chinese Sand Pears, suggesting a closer genetic relationship between Weixian pears in Group 1 and southern pear cultivars. The sequencing results of the non-coding region of chloroplast DNA showed that three more evolved haplotypes were detected in Weixian pears. The haplotype of most Weixian pears was haplotype H_3, while Weixian Hongli exhibited the haplotype H_2. Additionally, Xuehua and the Yali group, with the exception of Jinfeng Yali, displayed the haplotype H_1. By analyzing the genetic relationship and haplotype categories, we identified the genetic background of bud sport mutations and hybrids of Weixian pears. Jinfeng Yali belonged to the Yali group and had the characteristic of high self-fertility. Whole-genome resequencing analysis and chloroplast haplotype results showed that Yali, Meixiang Yali and Teda Yali belonged to the same branch and had the same haplotype. The clustering results and haplotype of Jinfeng Yali were different from these three Yali pear varieties. Jinfeng Yali was more closely related to Suanjiuli, and both had the same chloroplast haplotype, indicating that Jinfeng Yali was not a bud sport of Yali but possibly a selection from Yali seedlings. Dunzili and Baidunzili had a close genetic relationship and shared the same haplotype, suggesting Baidunzili may be a bud sport of Dunzili. The chloroplast haplotypes of Baihongli and Weixian Hongli were inconsistent, but they had a close relationship, suggesting that Weixian Hongli was more likely to be its paternal variety. Kaixinmian and Xiaohongmian shared the same chloroplast haplotype, and Xiaohongmian and Dunzili were in the same group, suggesting that Kaixinmian was a hybrid between Xiaohongmian and Dunzili. There was a distinct genetic difference between Youqiu and Wu'an Youqiu, despite their similar names. [Conclusion] In this study, based on the information of single nucleotide polymorphisms (SNPs) revealed by whole-genome resequencing and chloroplast DNA variation, we clarified the genetic relationship and background of Weixian pears. This result provides valuable references for protection and rational utilization of Weixian pear germplasm resources, further aiding in advancing the genetic understanding of pear cultivation in the region. Additionally, it enriches the cultural significance of pear culture in Weixian and offers cultural support for rural revitalization efforts.

Pear (Pyrus L.) is abundant in phenolic compounds which significantly contribute to functional properties. This study analyzed the phenolic profiles in the leaves of 460 pears using UPLC-MS/MS. A total of 28 phenolic compounds were identified, including one hydroxyphenyl-glucopyranoside, two hydroxycinnamates, five flavanols, four flavonoids, and sixteen flavonols, displaying pronounced species-specific and spatial variation. Arbutin emerged as the predominant phenolic component, accounting for 60.36 % of total phenolics, but was significantly less abundant in P. calleryana compared to others. European pears were richer in rutin, while Asian pears had higher concentrations of luteolin 7-O-glucoside. Chlorogenic acid levels showed a positive correlation with the varietal-origin altitude, while luteolin 7-O-glucoside and chrysoeriol 7-O-glucoside were negatively correlated with latitude. Varieties BT, YBMY, and XH_js003 exhibited high phenolic diversity, whereas JT41H, CPS, and ZYX possessed high arbutin. This study provides a comprehensive profile of pear phenolics, thereby enhancing their utilization in bioactives and understanding of adaptations.

The impact of maturity on pear fruit quality directly affects consumer taste. Ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was used to determine the sugar and organic acid components of mature pear fruits with different texture types, a texture analyzer was used to determine the texture traits of pear fruits. The result revealed that the variation tendency of sugar and organic acid components affected by the texture types, ripening stages and shelf-life. The decrease in flesh firmness of pear fruits was related to sucrose and glucose during the shelf-life of 0-14 days (d) at different ripening stages. According to the principal component analysis, Nanguoli, Jingbaili and Chili achieved the highest fruit quality score when harvested at 136 days after flower bloom (DAFB); Gute Luise and Korla pear achieved the highest fruit quality score when harvested at 146 DAFB; Yali and Dangshan Suli achieved the highest fruit quality score when harvested at 156 DAFB. In conclusion, combination of texture, sugar and organic acid components could serve as powerful maturity indicator candidates, provided valuable references for determining appropriate harvesting period and the best shelf-life quality of pear fruits.

BACKGROUND:Pyrus ussuriensis Maxim. are rich in nutrients, with a pleasant aroma and postharvest softening properties. Postharvest softening influences shelf life of fruit and fruit quality. Melatonin is a natural and safe preservative, which can effectively maintain fruit quality after harvesting, and delay softening of fruit. The aim of study was to elucidate mechanism of pear fruit softening and fruit aroma during postharvest storage and effect of melatonin. RESULTS:Ethylene production rate, respiration rate, weight loss of fruit, soluble solid content, titratable acidity were assessed, and transmission electron microscopy, metabolite profiling, and whole-transcriptome RNA-sequencing were performed. Four important pathways that pentose and glucuronate interconversion, galactose metabolism, sphingolipid metabolism and the starch and sucrose metabolism pathway were involved in pear fruit softening. Ethylene production pathway-related genes, such as ACS and ACO were involved in pear fruit softening and expression of that under exogenous melatonin treatment were slightly inhibited. Fruit aroma changed after storage mainly through lipoxygenase pathway under ddH2O treatment and exogenous melatonin treatment changed composition of volatile organic compounds. CeRNA networks associated with pear softening and aroma were established. Mdm-miR159a, mdm-miR396a/b-p3 and mdm-miR408a were found to modulate both fruit softening and aroma formation through ceRNA analysis. Mdm-miR10988-p3 was functionally diverse and as major regulatory components in ceRNA network. CONCLUSIONS:This study indicated that degradation of cell wall caused pear fruit softening, lipoxygenase pathway mainly affected change of fruit aroma during postharvest storage and exogenous melatonin treatment could improve fruit firmness after storage and alter pear's aroma. The mechanism underlying these effects was elucidated, providing theoretical basis for study of pear fruit softening and preservation technology.

Cold-storage is a widely-used technique for effectively maintaining pear quality. In this study, ultraperformance liquid chromatography tandem mass spectrometry (UPLC-MS/MS) was employed to determine sugar and organic acid components in pears of different textures after different cold-storage times, while texture analyzer was adopted to assess the texture traits of pear fruits. Different cold-storage times affected the quality of fruits from different pear varieties, whereas extended cold-storage led to quality deterioration. After cold-storage, the difference in sucrose between soft-flesh pears and crispy-flesh pears decreased and eventually faded with extended storage. Based on principal component analysis (PCA), Nanguoli, Jingbaili, Ruanerli, Korla pear, Chili and Yali achieved the highest fruit quality after 2 months of cold-storage, while Dangshan Suli and Shuihongxiao peaked after 4 months. This work provides a better strategy for determining suitable cold-storage time and shelf-life for pear varieties by comprehensively considering sugars, organic acids and texture variation.

Three-dimensional Spatial Transcriptomics has revolutionized our understanding of tissue regionalization, organogenesis, and development. However, existing approaches overlook either spatial information or experiment-induced distortions, leading to significant discrepancies between reconstruction results and in vivo cell locations, causing unreliable downstream analysis. To address these challenges, we propose ST-GEARS (Spatial Transcriptomics GEospatial profile recovery system through AnchoRS). By employing innovative Distributive Constraints into the Optimization scheme, ST-GEARS retrieves anchors with exceeding precision that connect closest spots across sections in vivo. Guided by the anchors, it first rigidly aligns sections, next solves and denoises Elastic Fields to counteract distortions. Through mathematically proved Bi-sectional Fields Application, it eventually recovers the original spatial profile. Studying ST-GEARS across number of sections, sectional distances and sequencing platforms, we observed its outstanding performance on tissue, cell, and gene levels. ST-GEARS provides precise and well-explainable 'gears' between in vivo situations and in vitro analysis, powerfully fueling potential of biological discoveries. Existing 3D Spatial Transcriptomics reconstruction approaches often overlook spatial information or experiment-induced distortions. Here, authors propose ST-GEARS to bridge the gap between in vivo cell locations and in vitro analysis, accurately recovering spatial profiles.

Understanding mammalian development heavily relies on classical animal models like the house mouse (Mus musculus). Advanced spatial transcriptomics has enabled biologists to break new ground in studies of molecular dynamics and cellular patterning during embryonic development with spatiotemporal resolution. To construct a comprehensive developmental trajectory, current three-dimensional (3D) spatial transcriptomic profiling leverages mouse embryos from gastrulation (E5.5) to organogenesis (E13.5) in continuity. However, a crucial phase for early organogenesis between E9.5 and E11.5 was deficient. To unveil the mystery of this stage, we present the 3D transcriptomics of mouse embryos at E9.5 and E11.5, with a widely applicable reconstruction workflow that bypasses sophisticated bioinformatic calculations. As our 3D atlas is generated at single-cell resolution, we demonstrate how organogenetic processes can be interpreted at different levels of granularity, from local cellular interactions to whole embryonic regionalization. We release the open-access database MOSTA3D (Mouse Organogenesis Spatiotemporal Transcriptomic Atlas in Three-dimensional) and hope a broader community will contribute to extending this framework from conception to senility in the near future. ### Competing Interest Statement The authors have declared no competing interest.

Cross-talks (e.g., host-driven iron withdrawal and microbial iron uptake between host gastrointestinal tract and commensal microbes) regulate immunotolerance and intestinal homeostasis. However, underlying mechanisms that regulate the cross-talks remain poorly understood. Here, we show that bacterial products up-regulate iron-transporter transferrin and transferrin acts as an immunosuppressor by interacting with cluster of differentiation 14 (CD14) to inhibit pattern recognition receptor (PRR) signaling and induce host immunotolerance. Decreased intestinal transferrin is found in germ-free mice and human patients with ulcerative colitis, which are characterized by impaired intestinal immunotolerance. Intestinal transferrin and host immunotolerance are returned to normal when germ-free mice get normal microbial commensalism, suggesting an association between microbial commensalism, transferrin, and host immunotolerance. Mouse colitis models show that transferrin shortage impairs host’s tolerogenic responses, while its supplementation promotes immunotolerance. Designed peptide blocking transferrin–CD14 interaction inhibits immunosuppressive effects of transferrin. In monkeys with idiopathic chronic diarrhea, transferrin shows comparable or even better therapeutic effects than hydrocortisone. Our findings reveal that by up-regulating host transferrin to silence PRR signaling, commensal bacteria counteract immune activation induced by themselves to shape host immunity and contribute for intestinal tolerance.

Accurate haplotyping facilitates distinguishing allele-specific expression, identifying cis-regulatory elements, and characterizing genomic variations, which enables more precise investigations into the relationship between genotype and phenotype. Recent advances in third-generation single-molecule long read and synthetic co-barcoded read sequencing techniques have harnessed long-range information to simplify the assembly graph and improve assembly genomic sequence. However, it remains methodologically challenging to reconstruct the complete haplotypes due to high sequencing error rates of long reads and limited capturing efficiency of co-barcoded reads. We here present a pipeline, AsmMix, for generating both contiguous and accurate diploid genomes. It first assembles co-barcoded reads to generate accurate haplotype-resolved assemblies that may contain many gaps, while the long-read assembly is contiguous but susceptible to errors. Then two assembly sets are integrated into haplotype-resolved assemblies with reduced misassembles. Through extensive evaluation on multiple synthetic datasets, AsmMix consistently demonstrates high precision and recall rates for haplotyping across diverse sequencing platforms, coverage depths, read lengths, and read accuracies, significantly outperforming other existing tools in the field. Furthermore, we validate the effectiveness of our pipeline using a human whole genome dataset (HG002), and produce highly contiguous, accurate, and haplotype-resolved assemblies. These assemblies are evaluated using the GIAB benchmarks, confirming the accuracy of variant calling. Our results demonstrate that AsmMix offers a straightforward yet highly efficient approach that effectively leverages both long reads and co-barcoded reads for haplotype-resolved assembly.

Precision mapping of site-specific glycans using mass spectrometry is vital in glycoproteomics. However, the diversity of glycan compositions across species often exceeds database capacity, hindering the identification of rare glycans. Here, we introduce pGlycoNovo, a software within the pGlyco3 software environment, which employs a glycan first-based full-range Y-ion dynamic searching strategy. pGlycoNovo enables de novo identification of intact glycopeptides with rare glycans by considering all possible monosaccharide combinations, expanding the glycan search space to 16 similar to 1000 times compared to non-open search methods, while maintaining accuracy, sensitivity and speed. Reanalysis of SARS Covid-2 spike protein glycosylation data revealed 230 additional site-specific N-glycans and 30 previously unreported O-glycans. pGlycoNovo demonstrated high complementarity to six other tools and superior search speed. It enables characterization of site-specific N-glycosylation across five evolutionarily distant species, contributing to a dataset of 32,549 site-specific glycans on 4602 proteins, including 2409 site-specific rare glycans, and uncovering unexpected glycan fragments.