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Malaxidinae is one of the most confusing groups in the Orchidaceae classification. Previous phylogenetic analyses have revealed that the relationships between the taxa in Malaxidinae have not yet been reliably established, using only a few plastome regions and nuclear ribosomal internal transcribed spacer (nrITS). In the present study, the complete plastomes of Oberonia integerrima and Crepidium purpureum were assembled using high-throughput sequencing. Combined with publicly available complete plastome data, this resulted in a dataset of 19 plastomes, including 17 species of Malaxidinae. The plastome features and phylogenetic relationships were compared and analyzed. The results showed the following: (1) Malaxidinae species plastomes possess the quadripartite structure of typical angiosperms, with sizes ranging from 142,996 to 158,787 bp and encoding from 125 to 133 genes. The ndh genes were lost or pseudogenized to varying degrees in six species. An unusual inversion was detected in the large single-copy region (LSC) of Oberonioides microtatantha. (2) Eight regions, including ycf1, matK, rps16, rpl32, ccsA-ndhD, clpP-psbB, trnF^GAA-ndhJ, and trnS^GCU-trnG^UCC, were identified as mutational hotspots. (3) Based on complete plastomes, 68 protein-coding genes, and 51 intergenic regions, respectively, our phylogenetic analyses revealed the genus-level relationships in this subtribe with strong support. The Liparis was supported as non-monophyletic. Full article

Cunninghamia lanceolata (Lamb.) Hook accounts for 12% of the total forest area in southern China, second only to Masson pine forests, and is an important part of the forest landscape in this region, which has a significant impact on the overall forest structure in southern China. In this study, we used kernel density analysis, landscape index calculation, variance test, and Markov prediction to analyze and forecast the evolution trend of landscape pattern in the central area of C. lanceolata in ten years. The objective is to investigate the change trend of the spatial pattern of C. lanceolata landscape in the long time series and its possible impact on zonal vegetation, as well as the macro-succession trend of C. lanceolata under the current social and economic background, and to make a scientific and reasonable prediction of its future succession trend. The current and future forecast results show that the landscape fragmentation degree of C. lanceolata is intensified, the erosion of bamboo forest is continuously intensified, and the landscape quality is continuously low. These results provide a reference for the future development direction of C. lanceolata and emphasize the need for targeted C. lanceolata management strategies in the future development of C. lanceolata, emphasizing the strengthening of monitoring, controlling harvesting, and managing bamboo competition in order to balance wood production with landscape quality and ecosystem stability. Full article

Dendrocalamus brandisii is a high-quality bamboo species that can be used for both bamboo shoots and wood. The nutritional components and flavors of D. brandisii vary from different geographical provenances. However, the unique biological characteristics of bamboo make morphological classification methods unsuitable for distinguishing them. Although the new cultivar ‘Manxie No.1’ has significant differences in the branch characteristics and the color of shoot sheaths compared to the D. brandisii, it still lacks precise genetic information at the molecular level. This study identified 231,789 microsatellite markers based on the whole genome of D. brandisii and analyzed their type composition and distribution on chromosomes in detail. Then, using TP-M13-SSR fluorescence-labeling technology, 34 pairs of polymorphic primers were screened to identify the new cultivar ‘Manxie No.1’ and 11 different geographical provenances of D. brandisii. We also constructed DNA fingerprinting profiles for them. At the same time, we mapped six polymorphic SSRs to the gene of D. brandisii, among which SSR673 was mapped to DhB10G011540, which is related to plant immunity. The specific markers selected in this study can rapidly identify the provenances and the new cultivar of D. brandisii and help explore candidate genes related to some important traits. Full article

The swnH1 gene in the endophytic fungus Alternaria oxytropis OW 7.8 isolated from Oxytropis glabra was identified, and the gene knockout mutant ΔswnH1 was first constructed in this study. Compared with A. oxytropis OW 7.8, the ΔswnH1 mutant exhibited altered colony and mycelium morphology, slower growth rate, and no swainsonine (SW) in mycelia, indicating that the function of the swnH1 gene promoted SW biosynthesis. Five differential expressed genes (DEGs) closely associated with SW synthesis were identified by transcriptomic analysis of A. oxytropis OW 7.8 and ΔswnH1, with sac, swnR, swnK, swnN, and swnH2 down-regulating. Six differential metabolites (DEMs) closely associated with SW synthesis were identified by metabolomic analysis, with P450, PKS-NRPS, saccharopine, lipopolysaccharide kinase, L-PA, α-aminoadipic, and L-stachydrine down-regulated, while L-proline was up-regulated. The SW biosynthetic pathways in A. oxytropis OW 7.8 were predicted and refined. The results lay the foundation for in-depth exploration of the molecular mechanisms and metabolic pathways of SW synthesis in fungi and provide reference for future control of SW in locoweeds, which would benefit the development of animal husbandry and the sustainable use of grassland ecosystems. Full article

Heat stress (HS) has become a common stressor, owing to the increasing frequency of extreme high-temperature weather triggered by global warming, which has seriously affected the reproductive capacity of important livestock such as sheep. However, little is known about whether HS reduces sperm motility by inducing circadian rhythm disorders in rumen microorganisms and metabolites in sheep. In this study, the year-round reproduction of two-year-old Hu rams was selected, and the samples were collected in May and July 2022 at average environmental temperatures between 18.71 °C and 33.58 °C, respectively. The experiment revealed that the mean temperature-humidity index was 86.34 in July, indicating that Hu rams suffered from HS. Our research revealed that HS significantly decreased sperm motility in Hu rams. Microbiome analysis further revealed that HS reshaped the composition and circadian rhythm of rumen microorganisms, leading to the circadian disruption of microorganisms that drive cortisol and testosterone synthesis. Serum indicators further confirmed that HS significantly increased the concentrations of cortisol during the daytime and decreased the testosterone concentration at the highest body temperature. Untargeted metabolomics analysis revealed that the circadian rhythm of rumen fluid metabolites in the HS group was enriched by the cortisol and steroid synthesis pathways. Moreover, HS downregulated metabolites, such as kaempferol and L-tryptophan in rumen fluid and seminal plasma, which are associated with promotion of spermatogenesis and sperm motility; furthermore, these metabolites were found to be strongly positively correlated with Veillonellaceae_UCG_001. Overall, this study revealed the relationship between the HS-induced circadian rhythm disruption of rumen microorganisms and metabolites and sperm motility decline. Our findings provide a new perspective for further interventions in enhancing sheep sperm motility with regard to the circadian time scale. Full article

As the main area for photosynthesis in trees, the canopy absorbs a large amount of carbon dioxide and plays an irreplaceable role in regulating the carbon cycle in the atmosphere and mitigating climate change. Therefore, monitoring the growth of the canopy is crucial. However, traditional field investigation methods are often limited by time-consuming and labor-intensive methods, as well as limitations in coverage, which may result in incomplete and inaccurate assessments. In response to the challenges encountered in the application of tree crown segmentation algorithms, such as adhesion between individual tree crowns and insufficient generalization ability of the algorithm, this study proposes an improved algorithm based on Mask R-CNN (Mask Region-based Convolutional Neural Network), which identifies irregular edges of tree crowns in RGB images obtained from drones. Firstly, it optimizes the backbone network by improving it to ResNeXt and embedding the SENet (Squeeze-and-Excitation Networks) module to enhance the model’s feature extraction capability. Secondly, the BiFPN-CBAM module is introduced to enable the model to learn and utilize features more effectively. Finally, it optimizes the mask loss function to the Boundary-Dice loss function to further improve the tree crown segmentation effect. In this study, TCSNet also incorporated the concept of panoptic segmentation, achieving the coherent and consistent segmentation of tree crowns throughout the entire scene through fine tree crown boundary recognition and integration. TCSNet was tested on three datasets with different geographical environments and forest types, namely artificial forests, natural forests, and urban forests, with artificial forests performing the best. Compared with the original algorithm, on the artificial forest dataset, the precision increased by 6.6%, the recall rate increased by 1.8%, and the F₁-score increased by 4.2%, highlighting its potential and robustness in tree detection and segmentation. Full article

As an important ecological barrier and a crucial base for animal husbandry in China, the forage–livestock balance in the Three-River-Source Region (TRSR) directly impacts both the degradation and recovery of grassland. This study examines the forage–livestock balance in the TRSR over the past 13 years (2010–2022) by calculating both the theoretical and actual livestock carrying capacity, thereby providing a scientific basis for regional animal husbandry policies. Firstly, the Carnegie–Ames–Stanford Approach (CASA) model was improved to fit the specific characteristics of alpine grassland ecosystem in the TRSR. This enhanced model was subsequently used to calculate the net primary productivity (NPP) of the grassland, from which the regional grassland yield and theoretical livestock carrying capacity were derived. Secondly, the actual livestock carrying capacity was calculated and spatialized based on the number of regional year-end livestock. Finally, the livestock carrying pressure index was determined using both the theoretical and actual livestock carrying capacity. The results revealed several key findings: (1) The average grassland NPP in the TRSR was 145.44 gC/m², the average grassland yield was 922.7 kg/hm², and the average theoretical livestock carrying capacity was 0.55 SU/hm² from 2010 to 2022. Notably, all three metrics showed an increasing trend over the past 13 years, which indicates the rise in grassland vegetation activities. (2) The average actual livestock carrying capacity over the 13-year period was 0.46 SU/hm², showing a decreasing trend on the whole. The spatial distribution displayed a pattern of higher capacity in the east and lower in the west. (3) Throughout the 13 years, the TRSR generally maintained a forage–livestock balance, with an average livestock carrying pressure index of 0.96 (insufficient). However, the trend of livestock carrying pressure is on the rise, with serious overloading observed in the western part of Qumalai County and the northern part of Tongde County. Slight overloading was also noted in Zhiduo, Maduo, and Zeku Counties. Notably, Tanggulashan Town, Zhiduo, Qumalai, and Maduo Counties showed significant increases in livestock carrying pressure, while Zaduo County and the eastern regions experienced significant decreases. In conclusion, this study not only provides feasible technical methods for assessing and managing the forage–livestock balance in the TRSR but also contributes significantly to the sustainable development of the region’s grassland ecosystem and animal husbandry industry. Full article

The GRAS gene family, derived from GAI, RGA, and SCR, plays a crucial role in plant growth and development. In the diploid Cyclocarya paliurus (2n = 2x = 32) with heterodichogamous characteristics, 51 CpGRAS genes were identified and phylogenetically classified into 10 subfamilies. Structural analysis revealed that CpGRAS genes possessed a canonical GRAS domain, but 70% lacked introns. WGD/segmental duplication was the major driver in the expansion of the CpGRAS family. In addition, a Ka/Ks ratio below 1 for these genes implied functional constraints and evolutionary conservation. Transcriptional profiling revealed significant differential expressions of CpGRAS genes between male and female flowers from two mating types, protogyny (PG) and protandry (PA). Notably, members of the DELLA subfamily exhibited significant upregulation in female flowers at the inflorescence elongation (S3) stage. The expression level of CpSCL6-2 in late-flowering samples (PA-F and PG-M) was higher than in early-flowering ones (PA-M and PG-F). Co-expression analysis identified that CpRGL1 and CpGAI-2 of the DELLA subfamily, along with CpSCL6-2, acted as hub genes, implying their crucial roles in floral development and potential involvement in the heterodichogamous flowering mechanism in C. paliurus. These findings broaden our understanding of CpGRAS genes and provide new insights into the molecular basis of heterodichogamy. Full article

Long-term and extensive mineral mining in the Kuermutu mine section of the Two Rivers Nature Reserve in the Altai region has disrupted the ecological balance between soil and vegetation. To assess the effectiveness of various restoration measures in this abandoned mine area, we compared two restoration approaches—natural turf transplantation (NTT) and replanted economic crop grassland (ARGC)—against an unaltered control (original grassland). We employed 11 evaluation indices to conduct soil and vegetation surveys. We developed a comprehensive evaluation model using the Analytic Hierarchy Process (AHP) to assess restoration outcomes for each grassland type. Our findings indicate that both NTT and ARGC significantly improved ecological conditions, such as reducing soil fine particulate matter loss and restoring vegetation cover. This brought these areas closer to their original grassland state. The species composition and community structure of the NTT and ARGC vegetation communities improved relative to the original grassland. This was due to a noticeable increase in dominant species’ importance value. Vegetation cover averaged higher scores in NTT, while the average height was greater in ARGC. The soil water content and soil organic carbon (SOC) varied significantly with depth (p < 0.05), following a general ‘V’ pattern. NTT positively impacted soil moisture content (SMC) at the surface, whereas ARGC influenced SMC in deeper layers, with the 40–50 cm soil layer achieving 48.13% of the original grassland’s SMC. SOC levels were highest in the control (original grassland), followed by ARGC and NTT, with ARGC showing the greatest organic carbon content at 20–30 cm depths. A comprehensive AHP ecological-economic evaluation revealed that restoration effectiveness scores were 0.594 for NTT and 0.669 for ARGC, translating to 59.4% and 66.9%, respectively. ARGC restoration was found to be more effective than NTT. These results provide valuable insights into ecological restoration practices for abandoned mines in Xinjiang and can guide future effectiveness evaluations. Full article

Using multi-view images of forest plots to reconstruct dense point clouds and extract individual tree parameters enables rapid, high-precision, and cost-effective forest plot surveys. However, images captured at close range face challenges in forest reconstruction, such as unclear canopy reconstruction, prolonged reconstruction times, insufficient accuracy, and issues with tree duplication. To address these challenges, this paper introduces a new image dataset creation process that enhances both the efficiency and quality of image acquisition. Additionally, a block-matching-based multi-view reconstruction algorithm, Forest Multi-View Reconstruction with Enhanced Confidence-Guided Dynamic Domain Propagation (CDP-MVS), is proposed. The CDP-MVS algorithm addresses the issue of canopy and sky mixing in reconstructed point clouds by segmenting the sky in the depth maps and setting its depth value to zero. Furthermore, the algorithm introduces a confidence calculation method that comprehensively evaluates multiple aspects. Moreover, CDP-MVS employs a decentralized dynamic domain propagation sampling strategy, guiding the propagation of the dynamic domain through newly defined confidence measures. Finally, this paper compares the reconstruction results and individual tree parameters of the CDP-MVS, ACMMP, and PatchMatchNet algorithms using self-collected data. Visualization results show that, compared to the other two algorithms, CDP-MVS produces the least sky noise in tree reconstructions, with the clearest and most detailed canopy branches and trunk sections. In terms of parameter metrics, CDP-MVS achieved 100% accuracy in reconstructing tree quantities across the four plots, effectively avoiding tree duplication. The accuracy of breast diameter extraction values of point clouds reconstructed by CDPMVS reached 96.27%, 90%, 90.64%, and 93.62%, respectively, in the four sample plots. The positional deviation of reconstructed trees, compared to ACMMP, was reduced by 0.37 m, 0.07 m, 0.18 m and 0.33 m, with the average distance deviation across the four plots converging within 0.25 m. In terms of reconstruction efficiency, CDP-MVS completed the reconstruction of the four plots in 1.8 to 3.1 h, reducing the average reconstruction time per plot by six minutes compared to ACMMP and by two to three times compared to PatchMatchNet. Finally, the differences in tree height accuracy among the point clouds reconstructed by the different algorithms were minimal. The experimental results demonstrate that CDP-MVS, as a multi-view reconstruction algorithm tailored for forest reconstruction, shows promising application potential and can provide valuable support for forestry surveys. Full article

The aim of this study was to investigate the effects of Lentilactobacillus plantarum (LP), cellulase (CE), and xylanase (XE) supplementation on the fermentation quality, chemical composition, and bacterial community of Caragana korshinskii Kom. silage. Four groups were designed for the study. No additives were used in the control group (CK), and LP (1 × 10⁶ cfu/g), CE (1 × 10⁴ IU/g) and XE (2 × 10⁵ IU/g) were added to the experimental groups on a fresh matter basis, with three replicates per group. To promote fermentation, 5% molasses was added to all of the groups. On days 15 and 60, fermentation quality, chemical composition and the bacterial community were analysed. The pH of groups CE and XE was lower than that of the CK group at 60 days. During ensiling, the lactic acid (LA) content in the experimental groups and the acetic acid (AA) content in the CK and LP groups increased. At 60 days, the dominant genera in the CK and LP groups was Weissella and the dominant genera in the CE and XE groups was Lentilactobacillus. At different times during silage, nucleotide metabolism was enhanced, whereas the metabolism of carbohydrate, amino acids, energy, cofactors and vitamins was inhibited in the LP group. However, the metabolism of amino acids, energy, cofactors and vitamins in the CE and XE groups was increased, whereas the metabolism of nucleotides was inhibited. In conclusion, LP, CE and XE could exert a positive effect on the fermentation quality of C. korshinskii Kom. silage by shifting the bacterial community composition. Full article

Non-native species have caused various problems for both animal and human communities globally, but their monitoring during the early stages of establishment is often difficult. A population of the Oriental Magpie (Pica serica) has established on Hokkaido Island, northern Japan, since the 1990s, offering a rare opportunity for field biologists to monitor the entire history of a colonizing avian population. To clarify the current number and distribution of the population and their major determinants, we conducted bimonthly surveys from May 2012 to March 2013, over a total of 417 h, in Tomakomai City, the central area of the current distribution. We found 181 to 248 magpies in every survey, and 46 active nests in May. Most of the magpies appeared in residential areas, avoiding commercial and industrial areas, and did not show seasonal changes in their distribution pattern. The magpies mainly foraged in short grasslands in public spaces, such as parks, in May and July, but most of the birds preferred house gardens for foraging from November to March. Dogs or cats were often kept outside in the gardens where the magpies foraged, and observations of magpies stealing and hoarding pet food were common. It is likely that the magpies rely on anthropogenic food resources such as pet food, especially in winter. Continuous monitoring of this population will enable further knowledge of the factors that limit the number and range of not only non-native species but also avian populations in general to be obtained. Full article

As a large agricultural country, China produces a large number of agricultural and sideline products while harvesting agricultural products every year. Crop straw is one of them. Broom sorghum is a traditional crop in China, which produces a large amount of straw resources every year. These straw resources are placed in the field and cannot be used efficiently. The purpose of this study was to solve the problem of straw utilization of Broom sorghum, one of the main food crops in arid and semi-arid areas of northern China. Broom sorghum is not only a nutritious food crop, its straw is also rich in crude fiber and mineral elements, which has high utilization value. However, due to the high content of lignocellulose in straw, the texture is hard, which limits its digestion and utilization efficiency as feed. In this study, the broom sorghum straw was used as the research object, and the straw raw materials were treated with Lactobacillus plantarum, cellulase and xylanase, respectively. After silage fermentation for 30 d and 60 d, the bags were opened to determine the nutritional quality, fermentation quality, microbial community structure and other indicators. The best fermentation time and additives for broom sorghum straw silage were comprehensively screened to improve the nutritional value of straw and animal production performance. The results showed that the nutritional quality of silage straw increased with the extension of fermentation time. Compared with silage straw after 30 days of fermentation, the nutritional quality and fermentation quality of straw were significantly improved after 60 days of fermentation. Lactobacillus plantarum, cellulase and xylanase could improve the silage performance of broom sorghum straw by improving the microbial community structure in straw, and the effect of cellulase was the best. When cellulase was used in straw at the standard of 20 U/g FM, the content of water-soluble carbohydrates could be significantly increased to 31.35 g/kg FM, and the concentration of lactic acid was also significantly increased to 23.79 g/kg FM. Therefore, in actual production, it is recommended to use cellulase at a dose of 20 U/g FM in broom sorghum silage and open the bag after 60 days of silage fermentation. The results of this study provided a scientific basis for the efficient utilization of broom sorghum straw as feed. Full article

The prevalence of plant parasitic nematodes (PPN) in the Irish peatlands was investigated in five different peatland habitats—raised bog, cutover scrub/woodlands, fens and peat grasslands, which were further sub-categorised into fourteen different sub-habitats. Within the raised bog habitat were healthy bog hummock (HBH), healthy bog lawn (HBL), degraded bog hummock (DBH) and degraded bog lawn (DBL) and the fen habitats were fen peat (FP) and rich fen peat (R-FP). Cutover scrub or woodland habitat included cutover scrub rewetted (C-RW), cutover scrub non-rewetted (C-NRW), woodlands rewetted (W-RW) and woodlands non-rewetted (W-NRW). Grassland included wasted peat (WP), rough grazing (RG-I) and improved fen peat grassland (IFPG-RW and IFPG-NRW). Soil samples from peatlands were all collected between July and December 2023 when the temperature ranged from 12 to 20 °C. One half of each sample was used for molecular nematode analysis and the other half for morphological identification of nematodes. For the morphological identification, a specific nematode extraction protocol was optimised for peatland soils, and the extracted nematodes were fixed onto slides to be studied under a high-power light microscope. Subsequently, the other part of the soil was processed to isolate total DNA, from which the 18S rRNA gene was sequenced for the identification of nematode taxa. The extracted DNA was also used for randomly amplified polymorphic DNA (RAPD) fingerprinting analysis to determine banding patterns that could classify different bog habitats based on PPN random primers. Compared to that in the climax habitats (HBH, HBL, DBH, DBL, FP, R-FP), PPN prevalence was recorded as being higher in grasslands (WP, RG-I, IFPG-RW and IFPG-NRW) and scrub/woodland ecosystems (C-RW, C-NRW, W-RW, W-NRW). The results indicate that nematode populations are different across the various bog habitats. Emerging and current quarantine PPN belonging to the families Pratylenchidae, Meloidogynidae, Anguinidae and Heteroderidae were noted to be above the threshold limits mentioned under EPPO guidelines, in grassland and wooded peatland habitats. Future actions for PPN management may need to be considered, along with the likelihood that these PPN might impact future paludiculture and other crops and trees growing in nearby agricultural lands. Full article

Aberrant DNA methylation plays a crucial role in breast cancer progression by regulating gene expression. However, the regulatory pattern of DNA methylation in long noncoding RNAs (lncRNAs) for breast cancer remains unclear. In this study, we integrated gene expression, DNA methylation, and clinical data from breast cancer patients included in The Cancer Genome Atlas (TCGA) database. We examined DNA methylation distribution across various lncRNA categories, revealing distinct methylation characteristics. Through genome-wide correlation analysis, we identified the CpG sites located in lncRNAs and the distally associated CpG sites of lncRNAs. Functional genome enrichment analysis, conducted through the integration of ENCODE ChIP-seq data, revealed that differentially methylated CpG sites (DMCs) in lncRNAs were mostly located in promoter regions, while distally associated DMCs primarily acted on enhancer regions. By integrating Hi-C data, we found that DMCs in enhancer and promoter regions were closely associated with the changes in three-dimensional chromatin structures by affecting the formation of enhancer–promoter loops. Furthermore, through Cox regression analysis and three machine learning models, we identified 11 key methylation-driven lncRNAs (DIO3OS, ELOVL2-AS1, MIAT, LINC00536, C9orf163, AC105398.1, LINC02178, MILIP, HID1-AS1, KCNH1-IT1, and TMEM220-AS1) that were associated with the survival of breast cancer patients and constructed a prognostic risk scoring model, which demonstrated strong prognostic performance. These findings enhance our understanding of DNA methylation’s role in lncRNA regulation in breast cancer and provide potential biomarkers for diagnosis. Full article