Genetica最新文献

Transposable elements (TEs) frequently generate incomplete derivative copies during transposition. The relative abundance of these variants is important in shaping the genomic landscape, but how these variants interact and compete within genomes remains poorly understood. To examine potential evolutionary conflicts among TE variants, we compared the replication behaviors of the full-length P element (FP) and one of its internally-deleted derivatives, the KP element, in Drosophila under three experimental conditions. KP elements were introduced into chromosomes at significantly higher frequencies than FP elements from a plasmid vector in both D. melanogaster and D. simulans. When both variants coexisted in D. simulans, KP elements also transposed between chromosomal sites more frequently than FP elements. Furthermore, the presence of KP elements reduced the long-term stability of FP elements in D. melanogaster. Together, these results demonstrate that KP elements possess an intrinsic replicative advantage over FP elements in competitive contexts, providing a mechanistic explanation for the global predominance of KP elements in D. melanogaster. This superiority is probably attributable to nucleotide sequence-specific properties of KP elements, rather than to differences in element size, genomic insertion position, or repression of transposition.

Retrocopies are processed copies of other genes that originate through reverse transcription and are randomly integrated into the genome. Once considered genomic "junk," emerging evidence shows they contribute to novel gene evolution and may aid adaptation to environmental and lifestyle changes. However, the role of retrocopies in the emergence of virulence in Plasmodium parasites remains largely unexplored. This study systematically characterizes retrocopies across 23 Plasmodium pathogenic genomes to elucidate their evolutionary origins, functional relevance, and potential contributions to the emergence of virulence. Using a stringent computational framework, we identified 724 high-confidence retrocopies exhibiting canonical signatures of retroposition. Retrocopies are frequently intact, under purifying selection, and often display detectable apparent transcription during intraerythrocytic stages, with a subset showing FPKM values from RNA-seq data comparable to or exceeding those of their parental genes, particularly in PPIase, PIR, and actin-related families linked to host interaction and immune evasion. Domain, GO, and KEGG enrichment analyses indicate that retrocopies are preferentially associated with processes such as cytoadhesion, chromatin remodeling, stress response, and cytoskeletal organization, and that retroposition has contributed to the expansion and diversification of pathogenic gene families in a lineage and host-specific manner. Ancestral state reconstruction indicates episodic gains and losses of retrocopies, with notable expansions in primate-infecting lineages. The findings show retrocopies in Plasmodium are widespread, evolutionarily dynamic, and functionally associated with key virulence-associated pathways rather than representing inert genomic byproducts. This study highlights retroposition as an underappreciated mechanism contributing to genomic plasticity in malaria parasites and provides a framework for future functional investigations.

N6-methyladenosine (m⁶A) is a prevalent modification of eukaryotic mRNAs that plays a crucial role in gene regulation and genome integrity. YT521-B homology (YTH) domain-containing RNA-binding proteins act as essential m6A readers, influencing the fate of m⁶A-modified RNAs through their involvement in RNA splicing, processing, stability, and translation. In plants, YTH genes regulate plant growth and development by modulating these post-transcriptional processes. Despite the significance of barley (Hordeum vulgare L) as a staple crop, the YTH genes in this species remain largely unexplored. We conducted a detailed analysis of the barley genome and identified 14 YTH genes. Phylogenetic classification categorized these genes into 5 distinct groups. These genes are distributed across seven chromosomes, and their predicted protein products are primarily localized within the nucleus. We observed conserved exon structures and domains among the various groups of HvYTHs. Analysis of the promoter region identified several regulatory elements associated with developmental processes, stress responses, and hormone regulation. Protein-protein interaction predictions suggested associations with m⁶A methyltransferase components and stress-responsive factors. Additionally, miRNA target analysis identified potential post-transcriptional regulators of HvYTH genes. Expression profiling using RNA-seq data revealed both tissue-specific and stress-responsive patterns. Several HvYTH genes showing differential expression under cold, heat, and heavy metal stress. qRT-PCR validation confirmed the upregulation of HvYTH8 across all stress conditions, while HvYTH5, HvYTH10, and HvYTH12 members exhibited stress-specific upregulation or downregulation. These results underscore the functional divergence of HvYTH genes in mediating abiotic stress tolerance, providing potential targets for improving barley resilience.

Understanding plant responses to abiotic stress is critical for improving stress resilience. Here, we performed an integrative analysis that uniquely converges three synergistic approaches: meta-analysis, consensus network analysis, and deep learning on Arabidopsis thaliana transcriptomic datasets under drought and salt conditions, comprising 64 samples across multiple studies. This novel framework allowed us to robustly identify 576 differentially expressed genes (397 upregulated, 170 downregulated), including At5g59310 (LTP4) as the most induced and At1g22690 (GASA9) as the most repressed. Functional annotation revealed that upregulated genes were enriched in stress-related pathways, including oxidoreductase and UDP-glycosyltransferase activities, while downregulated genes were associated with growth, hormone signaling, and photosynthesis. Among DEGs, 60 transcription factors spanning 15 families were identified, highlighting the central role of NAC, ERF, WRKY, bHLH, and bZIP families in stress regulation. Consensus co-expression network analysis revealed four modules with coordinated responses across both stresses, reflecting a growth-defense trade-off. Leveraging a deep learning pipeline featuring an Autoencoder for feature extraction and an MLP for classification, we distinguished stress versus normal samples with 94% accuracy and near-perfect AUC (0.992). Crucially, the convergence of these three methods pinpointed three high-confidence hub genes (At2g30250, At2g35070, and At2g30010), which were validated against independent RNA-seq datasets as core components of a general stress response. This work not only presents a powerful analytical blueprint but also delivers validated, high-priority genetic targets for direct application in engineering climate-resilient crops, with At2g35070 and At2g30010 emerging as particularly promising novel biomarkers.

Plasticity in meiotic recombination is a well-documented phenomenon with an unknown mechanism. Recent studies have shown variation in the magnitude and direction of plasticity with a putative connection to organismal stress. Though there have been many factors shown to contribute to recombination rate plasticity, dietary manipulations are understudied. Here we manipulated caloric density, which is known to contribute to well-known life-history trade-offs, to determine if it altered meiotic recombination rates. To investigate the role of genetic background, we selected two stocks from the Drosophila Genetic Reference Panel (DGRP) with varying susceptibility to starvation stress. We found that overall recombination rates increased as calories decreased consistent with previous dietary plasticity studies in Drosophila. Specifically, while neither 0.5x nor 2x were significantly different from the standard 1x diet, we found significant post hoc differences between the low-calorie (0.5x) versus the high-calorie (2x) dietary treatments in the strain DGRP_42 but not in DGRP_217, confirming the predicted increased sensitivity of DGRP_42 to starvation stress based on prior studies. In addition to measuring changes in crossover frequency and distribution, we also investigated various organismal reproductive and physiological traits. We found significant changes in female body mass, the number of oocytes in female ovaries, and male testis length due to both diet and genetic background. We also noted significant differences in DNA damage during oogenesis via TUNEL assay. Examination of ovarian gene expression confirmed that the strain that had plasticity in recombination (DGRP_42) also had 20x more differentially expressed genes between dietary treatments. Despite diet typically eliciting a tradeoff whereby dietary restriction increases lifespan, here we saw evidence that DGRP_42 did not experience benefits from low-calorie treatment, with evidence of stress response and increased DNA damage, which suggests plasticity in recombination is due to stress. Overall, our study provides additional support for the negative relationship between metabolism and recombination rate, differences between genetic backgrounds, and a connection between organismal traits and plasticity in meiotic recombination.