Genetica最新文献

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.

GPRC6A encodes a class C GPCR that can be activated by multiple ligands and potentially acts as a central regulator of diverse metabolic processes by modulating endocrine pathways. Experimental studies have reported numerous distinct functions for GPRC6A, suggesting it may be a key drug target for several metabolic disorders. Yet, the actual function of GPRC6A has been the focus of considerable debate due to contradictory results and the prevalence of loss-of-function mutations in human populations, leading to the perception of GPRC6A as a "Master of none". Interestingly, a genome-wide screen for gene loss events in vertebrate species identified the disruption of the GPRC6A gene in toothed whales, in contrast to widespread conservation in the closely related Bovidae family. We employ a synteny-informed comparative genomic approach to demonstrate that the loss of the GPRC6A gene among mammalian species is more widespread than previously reported, encompassing the entire Bovidae group within Artiodactyla and other fully aquatic mammals, including those belonging to Sirenia. An in-depth search of the genomes and short and long-read sequencing datasets of monotremes, hystricomorphs, rhinolophoid bats, pika, koala, and two shrews (white-toothed pygmy shrew and Asian house shrew) reveals at least nine independent GPRC6A gene loss events in vertebrates, highlighting its lineage-specific dispensability and raising questions regarding its ubiquitous functionality. The evolutionary loss of GPRC6A likely represents a lineage-specific response to specialised diets and ecological niches, reshaping metabolic regulation and taste perception and illuminating how niche specialisation influences gene retention or loss within the GPCR landscape across species.

The 2-oxoglutarate-dependent dioxygenase (2OGD) superfamily is critical for plant primary and secondary metabolism, but its evolutionary dynamics in radish (Raphanus sativus L.) remain uncharacterized. This study identified 165 radish 2OGD members with distinct physicochemical properties, including amino acid lengths ranging from 122 to 546, molecular weights from 13.1 to 60.1 kDa, and predominant subcellular localizations in the cytoplasm, nucleus, and chloroplast. Phylogenetic analysis clustered these 2OGD genes into 20 clades, functionally categorized into groups involved in hormone metabolism, flavonoid biosynthesis, and specialized metabolite synthesis. Chromosomal localization revealed uneven distribution across 9 chromosomes, with 89 pairs of segmental duplicates and significant syntenic relationships with Arabidopsis 2OGD genes, indicating expansion via gene duplication. Two ANS homologs, RsANS1 and RsANS2, in the LDOX clade were highly expressed in red radish taproots, their overexpression in Arabidopsis enhanced anthocyanin content.​ This study clarifies the evolutionary dynamics of the radish 2OGD superfamily, confirms the role RsANS1 and RsANS2 in anthocyanin biosynthesis, and lays a foundation for investigating the functions of 2OGD genes in regulating metabolite diversification and phenotypic development in radish.

The whole mitochondrial genomes (mitogenomes) excluding the control region were sequenced for 42 samples of the ten species of scincid lizards of the genus Plestiodon occurring in Japan, and the mitochondrial genealogy of the East Asian Plestiodon was reconstructed on the basis of the mitogenomic dataset. A comparison with a species phylogeny based on five nuclear DNA fragments revealed that P. latiscutatus, a species distributed on the Izu Peninsula of the Japanese Main Islands, was a sister to the clade consisting of P. japonicus and P. finitimus, species occurring in the remaining parts of the Main Island in the species phylogeny, whereas the former species was a sister to the P. capito group occurring in continental China in the mitogenomic phylogeny. A tree reconciliation analysis of the species and the mitochondrial phylogenies revealed horizontal transfer of mitochondria, suggesting that the position of P. latiscutatus was caused by past introgression of mtDNA from the ancestral P. capito group to the ancestral P. latiscutatus. This further suggests a past long-distance dispersal of the skink from the Eurasian continent to the Izu Peninsula and Izu Islands beyond the western part of the Japanese Main Islands in the Miocene.

Actin, one of the most highly conserved and ubiquitous proteins found in all eukaryotes, serves as the primary component of microfilaments. These cytoskeletal elements provide structural support to cells while actively regulating diverse biological processes. Despite the agricultural significance of soybean (Glycine max) as a global legume crop, systematic characterization of its actin gene family remains unexplored. Through comprehensive bioinformatic analysis, we identified 18 soybean actin genes (designated GmACT1-GmACT18) unevenly distributed across 13 of the 20 soybean chromosomes. Phylogenetic analysis classified these genes into five distinct subclasses, with members within each subclass sharing conserved gene structures and protein sequences. All GmACT genes encode predicted polypeptides of 377 amino acids, which display pairwise sequence similarities exceeding 93.10%. Promoter analysis identified many cis-acting elements regulating hormonal and stress responses, underscoring their vital roles in growth and environmental adaptation. Genome synteny analysis identified 29 paralogous GmACT gene pairs, with calculated Ka/Ks ratios (< 0.04) indicating robust purifying selection during gene family expansion. Sequence alignment identified 36 amino acid substitutions among GmACT proteins, including 25 subclass-specific residues that may lead to divergence in biochemical properties. Transcriptome analysis identified distinct spatiotemporal expression patterns, among which GmACT1, 4, 9, 15, and 16 showed consistently high expression not only in all organs and tissues but also under diverse biotic and abiotic stresses, demonstrating their robust and stable expression profile. This constitutive expression suggests these genes are excellent candidates for use as internal controls in gene expression studies. Several GmACT members exhibited stress-responsive expression patterns, implying specialized roles in abiotic/biotic stress adaptation. This systematic investigation establishes fundamental insights into soybean actin genes, laying crucial groundwork for their future functional studies.

Santalum album L. (Sandalwood) is a commercially and medicinally significant tree species native to India and is widely distributed across Asia and Australia. Valued for its high-quality heartwood and essential oil, sandalwood plays a vital role in the pharmaceutical, cosmetic, and cultural industries. India contributes to more than 85% of global production, but natural populations have sharply declined due to overexploitation, habitat loss, and disease pressures. Recent genomic advancements, including chromosome-level genome assembly, transcriptomics, and proteomics, have provided critical insights into oil biosynthesis, heartwood formation, and stress response mechanisms. Studies have identified key transcription factors, such as MYB and WRKY; gene families, such as TPS and SAUR; and enzymes involved in secondary metabolism and abiotic stress tolerance. Molecular markers such as SSRs and SNPs have enabled the assessment of genetic diversity and structure across native and introduced populations, informing conservation and breeding programs. Functional genomic studies have also highlighted the importance of genotype-specific expression profiles for enhancing oil yield and climate resilience. Despite these advancements, key research gaps persist, including limited application of genomic tools in breeding, lack of functional gene validation, lack of CRISPR-based gene editing, and scanty early biomarkers. However, integrated silvicultural-genomic strategies, structured germplasm conservation, and supportive policies are crucial for enhancing productivity, resilience, and sustainable sandalwood cultivation. Therefore, the future research should focus on genome-assisted selection, CRISPR-based gene editing, and the development of functional markers for trait prediction. This review emphasizes the importance of multidisciplinary research in securing the long-term ecological and economic viability of S. album, addressing both production gaps and conservation challenges in the face of global climate change.