Search Results (10)

Background: Plant mitochondrial genomes exhibit extreme variation in size and structure while maintaining a conserved set of core protein-coding genes. This combination of structural diversity and functional conservation provides valuable insights into evolutionary processes such as genome expansion, rearrangement, and intracellular DNA transfer. Curcuma longa, an economically and medicinally important species in the genus Curcuma (Zingiberaceae), has not yet been studied in terms of the organization and evolution of its mitochondrial genome. Methods: In this study, we assembled and annotated the mitochondrial and plastid genomes of C. longa using third-generation HiFi sequencing data, systematically analyzing their genomic structure, repetitive sequence content, and features of sequence transfer between nuclear and organellar genomes. Results: The mitochondrial genome of C. longa was assembled as a complex, network-like structure consisting of 12 contigs with a total length of approximately 7.7 Mb, making it one of the largest mitochondrial genomes reported in monocots to date. Comparative analysis revealed significant differences in repeat types, abundance, and length distribution between the two organellar genomes. Additionally, extensive intracellular DNA transfer events were identified among the nuclear, mitochondrial, and plastid genomes. Conclusions: Overall, this study provides the first comprehensive report on the giant mitochondrial genome of C. longa, detailing its structural organization, repeat content, and intergenomic transfers. These findings lay a foundation for understanding mitochondrial genome evolution in Curcuma and offer broader insights into the mechanisms driving extreme mitochondrial genome expansion in angiosperms and monocots specifically. Full article

Finger vein recognition algorithms based on deep learning techniques are widely used in many fields. However, the training of finger vein recognition models is hindered by privacy issues and the scarcity of public datasets. Although applying federated learning techniques to finger vein recognition can effectively address privacy concerns, data heterogeneity across clients limits the performance of the models, especially on small datasets. To address these problems, in this paper, we propose a new federated finger vein recognition algorithm (FedPSFV). The algorithm is based on the federated learning framework, which increases the interclass distance of each dataset by sharing the prototypes among clients to solve the data heterogeneity problem. The algorithm also integrates and improves the margin-based loss function, which advances the feature differentiation ability of the model. Comparative experiments based on six public datasets (SDUMLA, MMCBNU, USM, UTFVP, VERA, and NUPT) show that FedPSFV has better accuracy and generalizability; the TAR@FAR = 0.01 is improved by 5.00–11.25%, and the EER is reduced by 81.48–90.22% compared to the existing methods. Full article

User authentication is crucial for safeguarding access to digital systems and services. Biometric authentication serves as a strong and user-friendly alternative to conventional security methods such as passwords and PINs, which are often susceptible to breaches. This study proposes a deep learning-based multimodal biometric system that combines fingerprint (FP) and finger vein (FV) modalities to improve accuracy and security. The system explores three fusion strategies: feature-level fusion (combining feature vectors from each modality), score-level fusion (integrating prediction scores from each modality), and a hybrid approach that leverages both feature and score information. The implementation involved five pretrained convolutional neural network (CNN) models: two unimodal (FP-only and FV-only) and three multimodal models corresponding to each fusion strategy. The models were assessed using the NUPT-FPV dataset, which consists of 33,600 images collected from 140 subjects with a dual-mode acquisition device in varied environmental conditions. The results indicate that the hybrid-level fusion with a dominant score weight (0.7 score, 0.3 feature) achieved the highest accuracy (99.79%) and the lowest equal error rate (EER = 0.0018), demonstrating superior robustness. Overall, the results demonstrate that integrating deep learning with multimodal fusion is highly effective for advancing scalable and accurate biometric authentication solutions suitable for real-world deployments. Full article

The application of urease inhibitors (UIs) and optimizing nitrogen (N) split application ratio (NSR) can both minimize ammonia (NH₃) volatilization and increase rice yield. However, few studies have analyzed the combined effects of these two practices with straw returning on rice yield and NH₃ volatilization. In this study, based on a field experiment involving rice yield, aboveground dry matter (ADM), crop N uptake (N_upt), and NH₃ volatilization from 2018 to 2019 in Sichuan Basin, China, the WHCNS (soil water heat carbon nitrogen simulator) model was used to simulate the effects of straw returning, UI, and NSR on rice growth and NH₃ volatilization. The results showed that the WHCNS model performed well in simulating rice growth and NH₃ volatilization. With straw return amount exceeding 4 t ha⁻¹, rice yield increased slowly or stabilized, while N_upt and NH₃ volatilization continued to increase. Increasing the panicle fertilizer (PF) proportion enhanced N_upt during the PF stage, thereby promoting yield improvement. The NSR₃ (a 1:1:3 ratio of base fertilizer, tiller fertilizer, and PF) achieved the highest yield, exceeding that of 2:1:2 by 0.29, 0.23, and 0.08 t ha⁻¹ at straw return amounts of 2, 3, and 4 t ha⁻¹, respectively. However, the effects of UI on N_upt and yield enhancement were limited. Furthermore, optimized NSR and the application of UI reduced NH₃ volatilization during the basal or tiller fertilizer stages, leading to an average decrease of 5.5% and 8.5% in total NH₃ volatilization, respectively. Meanwhile, the increase in straw return amount reduced the NH₃ volatilization reduction effects of both practices. Overall, the combination of NSR₃ and UI with the straw return amount of 3 t ha⁻¹ was the optimal practice for balancing food security and environmental benefits in purple soil area. Full article

Biofuels play an important role in the reduction of greenhouse gas emissions, but their production results in greenhouse gases such as nitrous oxide (N₂O), mainly from nitrogen (N) fertilization. Brassica carinata (carinata) is an unexplored winter crop in the world’s main cropping areas, with multiple applications (cover crop, jet biofuel, and animal feed, among others). We analyzed a set of on-farm fertilization experiments (2016–2018) in southern South America using quantile regression to establish a baseline for both seed yield (Y_SEED) and the different components of nitrogen-use efficiency (NUE). Maximum Y_SEED for the 50th and 90th percentiles ranged from 2.5 to 3.5 Mg ha⁻¹, with a N availability of 150–160 kg ha⁻¹ (soil + fertilization). The NUE ranged from 3 to 13 kg seed per kg of N available. Carinata, in the absence of other limiting factors, had a high N uptake (N_UPT) capacity (1.0 to 1.5 kg ha⁻¹ N_UPT per kg ha⁻¹ N available [soil + fertilization]). The explored N fertilization rates had no significant influence on oil concentrations (455 to 517 g kg⁻¹) and protein concentrations (192 to 253 g kg⁻¹). The region has a high potential for carinata production, with a high capacity to take up available N. Full article

DNA originating from organellar genomes are regularly discovered in nuclear sequences during genome assembly. Nevertheless, such insertions are sometimes omitted during the process of nuclear genome assembly because the inserted DNA is assigned to organellar genomes, leading to a systematic underestimation of their frequency. With the rapid development of high-throughput sequencing technology, more inserted fragments from organelle genomes can now be detected. Therefore, it is necessary to be aware of the insertion events from organellar genomes during nuclear genome assembly to properly attribute the impact and rate of such insertions in the evolution of nuclear genomes. Here, we investigated the impact of intracellular gene transfer (IGT) from the plastome to the nuclear genome using genome assemblies that were refined through time with technological improvements from two model species, Arabidopsis thaliana and Oryza sativa. We found that IGT from the plastome to the nuclear genome is a dynamic and ongoing process in both A. thaliana and O. sativa, and mostly occurred recently, as the majority of transferred sequences showed over 95% sequence similarity with plastome sequences of origin. Differences in the plastome-to-nuclear genome IGT between A. thaliana and O. sativa varied among the different assembly versions and were associated with the quality of the nuclear genome assembly. IGTs from the plastome to nuclear genome occurred more frequently in intergenic regions, which were often associated with transposable elements (TEs). This study provides new insights into intracellular genome evolution and nuclear genome assembly by characterizing and comparing IGT from the plastome into the nuclear genome for two model plant species. Full article

Growing amounts of genomic data and more efficient assembly tools advance organelle genomics at an unprecedented scale. Genomic resources are increasingly used for phylogenetic analyses of many plant species, but are less frequently used to investigate within-species variability and phylogeography. In this study, we investigated genetic diversity of Fagus sylvatica, an important broadleaved tree species of European forests, based on complete chloroplast genomes of 18 individuals sampled widely across the species distribution. Our results confirm the hypothesis of a low cpDNA diversity in European beech. The chloroplast genome size was remarkably stable (158,428 ± 37 bp). The polymorphic markers, 12 microsatellites (SSR), four SNPs and one indel, were found only in the single copy regions, while inverted repeat regions were monomorphic both in terms of length and sequence, suggesting highly efficient suppression of mutation. The within-individual analysis of polymorphisms showed >9k of markers which were proportionally present in gene and non-gene areas. However, an investigation of the frequency of alternate alleles revealed that the source of this diversity originated likely from nuclear-encoded plastome remnants (NUPTs). Phylogeographic and Mantel correlation analysis based on the complete chloroplast genomes exhibited clustering of individuals according to geographic distance in the first distance class, suggesting that the novel markers and in particular the cpSSRs could provide a more detailed picture of beech population structure in Central Europe. Full article

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria. Full article

The transfer of genetic material from the mitochondria and plastid to the nucleus gives rise to nuclear integrants of mitochondrial DNA (NUMTs) and nuclear integrants of plastid DNA (NUPTs). This frequently occurring DNA transfer is ongoing and has important evolutionary implications. In this review, based on previous studies and the analysis of NUMT/NUPT insertions of more than 200 sequenced plant genomes, we analyzed and summarized the general features of NUMTs/NUPTs and highlighted the genetic consequence of organellar DNA insertions. The statistics of organellar DNA integrants among various plant genomes revealed that organellar DNA-derived sequence content is positively correlated with the nuclear genome size. After integration, the nuclear organellar DNA could undergo different fates, including elimination, mutation, rearrangement, fragmentation, and proliferation. The integrated organellar DNAs play important roles in increasing genetic diversity, promoting gene and genome evolution, and are involved in sex chromosome evolution in dioecious plants. The integrating mechanisms, involving non-homologous end joining at double-strand breaks were also discussed. Full article

Genotypic variation in N efficiency defined as high grain yield under limited nitrogen (N) supply of winter oilseed-rape line-cultivars has been predominantly attributed to N uptake efficiency (NUPT) through maintained N uptake during reproductive growth related to functional stay-green. For investigating the role of stay-green, N retranslocation and N uptake during the reproductive phase for grain yield formation, two line cultivars differing in N starvation-induced leaf senescence were grown in a field experiment without mineral N (N0) and with 160 kg N·ha⁻¹ (N160). Through frequent harvests from full flowering until maturity N uptake, N utilization and apparent N remobilization from vegetative plant parts to the pods could be calculated. NUPT proved being more important than N utilization efficiency (NUE) for grain yield formation under N-limiting (N0) conditions. For cultivar differences in N efficiency, particularly N uptake during flowering (NUPT) and biomass allocation efficiency (HI) to the grains, were decisive. Both crop traits were related to delayed senescence of the older leaves. Remobilization of N particularly from stems and leaves was more important for pod N accumulation than N uptake after full flowering. Pod walls (high N concentrations) and stems (high biomass) mainly contributed to the crop-residue N at maturity. Decreasing the crop-inherent high N budget surplus of winter oilseed-rape requires increasing the low N remobilization efficiency particularly of pod-wall N to the grains. Addressing this conclusion, multi-year and -location field experiments with an extended range of cultivars including hybrids are desirable. Full article