Genetica最新文献

The complete mitochondrial genome of the endangered spotted eagle ray, Aetobatus ocellatus, was determined for the first time using Next Generation Sequencing (NGS) reads mined from the Sequence Read Archive (SRA) of the GenBank database (BioSample SAMN31811701, collection site: Bohol Island, Philippines). The mitogenome of the spotted eagle ray (GenBank accession BK072016) is 20,217 bp in length and exhibits a typical vertebrate mitogenome organization, consisting of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a control region. A phylogenetic analysis based on the nucleotide sequences of 13 protein-coding genes from different related species confirmed the species status and classification of A. ocellatus as an Indo-West Pacific species. This species was formerly described as A. narinari, which is now recognized as being restricted to the Atlantic Ocean. The findings of this study provide significant insights into the complex taxonomic and phylogenetic relationships of Aetobatidae. They may further assist in conservation strategies and help resolve taxonomic uncertainties concerning the classification of species within Aetobatidae, which remains under debate.

Phylogenomic approaches effectively minimize topological incongruences caused by heterogeneous gene evolutionary rates among lineages. The taxonomic status of Breynia, Glochidion, Synostemon, and Sauropus-whether they should be merged into Phyllanthus or retain their separate generic status-remains controversial. Moreover, these taxonomic revisions lack evidences from phylogenomic evidence. In this study, we assembled the first complete plastid genomes of Breynia disticha, Glochidion eriocarpum, G. hirsutum, G. lanceolarium, Phyllanthus fluitans, Sauropus androgynus, and Synostemon bacciformis to elucidate plastome evolutionary dynamics and resolve phylogenetic relationships among these five genera. The plastomes ranged in size from 152,927 to 157,460 bp, encoding a conserved set of 78 protein-coding genes, 35-36 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes, totaling 117-118 unique genes. Notably, 12 novel tRNA secondary structures were identified, potentially linked to lineage-specific adaptations. Structural variation at the LSC/IRb boundary, driven by IRb expansion-contraction dynamics, resulted in significant gene length and content heterogeneity. Divergence hotspot analyses identified petA-psbJ, rpl22, ndhF-rpl32, and ycf1 as hypervariable loci suitable for DNA barcoding applications. Positive selection signals were detected in five genes (ndhB, rpl33, rps15, ycf2, ycf4), suggesting their critical roles in environmental adaptation. Phylogenomic discordance between plastid and nuclear ribosomal DNA (nrDNA) datasets was pervasive across Breynia, Glochidion, Phyllanthus, Sauropus, and Synostemon, likely attributable to historical hybridization or chloroplast capture events. Given that the intergeneric boundaries among Breynia, Glochidion, Phyllanthus s.s., Sauropus, and Synostemon are obscure and that extensive cytonuclear discordance exists, we recommend accepting a broad circumscription of Phyllanthus.

The MADS-box transcription factor (TF) superfamily, one of the largest gene groups in plants, is essential for regulating stress responses. However, its function in rice under pesticide stress remains unknown. To address this gap, we investigated the traits and roles of the rice MADS-box gene family under pesticide exposure. Transcriptome analysis of rice (Oryza sativa) treated with fluroxypyr-meptyl (FLUME) and oxyfluorfen (OFF) revealed 30 OsMADS-box genes and 3 MADS-box differentially expressed genes (DEGs). Phylogenetic analysis classified these genes into 12 subfamilies: Mα, Mβ, Mγ, SOC1, E, A, AGL12, SVP, ANR1, Bs, B, and MIKC*. Chromosomal mapping revealed uneven distribution of OsMADS-box genes across all 12 chromosomes, with segmental duplication contributing to gene family expansion. Collinearity analysis identified 14 orthologous gene pairs within rice and additional orthologous gene pairs shared with other plant species: 4 with Arabidopsis (Arabidopsis thaliana), 17 with soybean (Glycine max), 45 with maize (Zea mays), and 36 with wild sugarcane (Saccharum spontaneum). Structural analysis showed that OsMADS-box genes possess diverse gene architectures, cis-acting elements, motif compositions, and conserved domains, enabling responses to biotic and abiotic stress. Docking studies of OFF, FLUME, and the three MADS-box DEGs identified key amino acid residues implicated in pesticide binding. qRT-PCR confirmed preferential expression of several MADS-box DEGs under OFF- and FLUME-induced stress. Protein-protein interaction network analysis further supported the involvement of OsMADS-box proteins in FLUME and OFF metabolism. These findings provide insights into the OsMADS-box superfamily and offer valuable resources for functional studies on their roles in pesticide metabolism.

The c-kit-ligand (KITLG) is a pigmentation gene that has a strong selection signal in the majority of domestic animals. Recent studies in human and rodent populations have indicated a role for KITLG in the response to social stress. Regression analysis revealed three significant predictors of KITLG minor allele frequency (MAF) in domestic goat populations: urbanization level (β = +0.0037, p < 0.001), latitude (β = +0.0019, p = 0.010), and solar radiation (β = -0.00029, p < 0.001). Together, these factors explained 53.6% of the variation in the KITLG gene MAF (adjusted R² = 0.527). The results obtained indicate a complex influence of anthropogenic and natural factors on the genetic structure of domestic goat populations. We used local urbanization level as an indirect indicator of human-animal relationship, suggesting that the KITLG pleiotropy links human-recognizable pigmentation patterns to certain behavioural phenotypes. This association can be considered as a possible mechanism for facilitating and maintaining domestication.

Population genetics plays a critical role in creating policies for managing fisheries, conservation, and development of aquaculture. The golden snapper, Lutjanus johnii (Bloch, 1792), is a highly commercial and aquaculture important snapper species. This study used mitochondrial markers D-loop (151 specimens) and Cytochrome b (Cyt-b, 120 specimens) from 10 populations, including populations from the east South China Sea, the west South China Sea and the Strait of Malacca to investigate the genetic diversity, population connectivity, and historical demography of L. johnii. High levels of haplotype diversity (D-loop: 0.974-1.000; Cyt-b: 0.711-0.952) were observed along with low nucleotide diversity (D-loop: 0.009-0.052; Cyt-b: 0.001-0.007), which suggests a population bottleneck was followed by an abrupt rise in population size. Genetic structuring was identified between populations in the South China Sea and its adjacent waters, compared to those in the Kuala Kedah population. Genetic structuring was consistently inferred from Bayesian inference trees, median joining networks (MJN), population pairwise Ф_ST comparisons, F_ST indices of genetic differentiation and a hierarchical AMOVA (Analysis of Molecular Variance). Demographic neutrality statistics and DNA mismatch distributions revealed species went through a sudden demographic expansion. Throughout the Pleistocene. Result from this study suggest that fisheries management for this species should take into consideration the genetic and demographic independence of the Kuala Kedah population. Policymaking should adhere to the precautionary principle to safeguard potential adaptive genetic diversity and ensure the sustainability of regional and local fisheries.

Bacteria are constantly exposed to diverse environmental stresses, necessitating complex adaptive mechanisms for survival. Thermus thermophilus, a thermophilic extremophile, serves as an excellent model for investigating these responses due to its remarkable resilience to harsh conditions. Recent advances in artificial intelligence, particularly in machine learning, have transformed the identification of novel stress-responsive biomarkers. In this study, we analyzed transcriptomic data from 65 T. thermophilus HB8 samples subjected to various abiotic stresses to identify key genes involved in stress adaptation. We applied a suite of supervised machine learning algorithms to classify samples and prioritize informative features. Among the tested models, Extreme Gradient Boosting (XGBoost) and Random Forest (RF) achieved the highest classification performance, with XGBoost attaining perfect discrimination between stressed and control samples (AUC = 1.00) and RF closely following (AUC = 0.99). Feature importance analysis consistently identified three candidate genes: TTHA0029, TTHA1720, and TTHA1359. Functional validation using RT-qPCR confirmed the significant upregulation of TTHA0029 and TTHA1720 under salt and hydrogen peroxide stress, suggesting roles in redox regulation and ionic homeostasis. Phylogenetic analysis further revealed the specificity of these genes to the Thermus genus. Overall, our findings highlight central molecular players in stress tolerance in T. thermophilus and demonstrate the utility of machine learning in biomarker discovery. The identified genes, TTHA0029 and TTHA1720, may serve as promising targets for genetic engineering to improve stress resilience in both crops and industrially relevant microorganisms.

Understanding the genetic structure of wild ungulate populations is essential for informed conservation planning, particularly in ecologically sensitive and topographically complex landscapes such as the Himalayas. We investigated the genetic variation in Bharal (Pseudois nayaur) populations from the western (WH) and eastern Himalayas (EH) using eight microsatellite loci. Our analysis revealed significant genetic divergence between WH and EH populations, with a Nei's genetic distance of 0.91 and a pairwise FST value of 0.14, indicating their delineation as distinct lineages. WH populations showed greater genetic affinity with the Himalayan Bharal (P. n. nayaur). In contrast, EH populations were closely related to the Chinese Bharal (P. n. szechuanensis) of the Tibetan Plateau. Hence, WH and EH Bharal represent distinct Evolutionarily Significant Units (ESUs) and should be managed as separate Management Units (MUs). It further highlighted the need for region-specific conservation strategies to safeguard the genetic integrity and ecological resilience of Bharal populations across the Indian Himalayan Region.

Thaumatin-Like Proteins (TLPs) play a crucial role against biotic and abiotic stresses, acting as signaling molecules in transduction pathways and exhibiting antimicrobial activity. The present study aimed to characterize TLPs of Cenostigma pyramidale (Fabaceae) and analyze their expression (RNA-Seq) in root tissues under salt stress. A total of 36 CpTLPs were identified, which showed the characteristic TLP domain and a signal peptide in the N-terminal region. Multiple sequence alignment revealed the conservation of 16 cysteine residues, a signature motif, and a "REDDD" motif, all characteristic of TLPs. Three typical TLPs domains were identified in the three-dimensional modeling of the six analyzed sequences. The molecular dynamics simulation revealed stability along most of these sequences. RNA-seq under salt stress showed that six C. pyramidale TLPs (CpTLP2, CpTLP3, CpTLP5, CpTLP17, CpTLP20, and CpTLP31) were differentially expressed. The RT-qPCR expression validation was performed in leaf and root tissues (30 min, 2 h, and 11 days after salt stress). In leaf tissue, most CpTLPs were induced in at least one time point analyzed. In root tissue, we observed validation of the RNA-Seq expression data of CpTLP3, CpTLP5, CpTLP20, and CpTLP31, as well as distinct expression patterns between leaf and root tissues. Our results showed significant variations in the transcriptional response of the TLP family across different plant tissues and associated specific genes of this family with salt tolerance in C. pyramidale. These findings enhance the understanding of the role of TLPs in salt stress and may be useful in genetic improvement strategies to increase salt tolerance.

Universal Stress Proteins (USPs) are widely distributed across various organisms and play a crucial role in survival under stress conditions. As environmental stresses become more severe, understanding the role of USPs in developing stress-resistant plants has gained increasing importance. In this study, we identified 231 USP-coding genes in the genomes of Brassica napus (BnUSP1-BnUSP115), B. rapa (BrUSP1-BrUSP54), and B. oleracea (BoUSP1-BoUSP62) using bioinformatics approaches. Phylogenetic analysis grouped these genes into six distinct clusters based on bootstrap values. Structural analysis of USP genes in these Brassica species revealed variability in intron numbers, with phase 0 introns being more prevalent than phases 1 and 2. Gene duplication analysis showed that segmental/WGD duplication events significantly contributed to the expansion of the USP gene family, with duplicated genes undergoing purifying selection. Promoter analysis identified several cis-regulatory elements related to stress and hormone responses-such as MYB, MYC, ARE, ERF, ABRE, TGA-element, and TCA-element-in the upstream regions of BnUSP, BoUSP, and BrUSP genes, suggesting their involvement in complex stress response pathways. Finally, RNA-seq data were used to examine the expression patterns of BnUSP genes across different tissues (root, stem, seed, flower, pod, and leaf) and under various abiotic stresses (cold, salinity, dehydration, and ABA). Their responses to salt stress were further validated using qRT-PCR. These analyses identified BnUSP60 and BnUSP2 as potential targets for breeding programs aimed at enhancing stress resistance in B. napus.

Phyllanthus fluitans, a member of the Phyllanthaceae, is a unique free-floating aquatic species exhibiting considerable ornamental value. In this study, we assembled the mitochondrial genome of P. fluitans representing the first mitochondrial genome report of the Phyllanthaceae family. The mitogenome comprises two circular chromosomes spanning 230,785 bp (chromosome 1) and 143,421 bp (chromosome 2), collectively harboring 32 protein-coding genes (PCGs), 25 tRNA genes, four rRNA genes, and one pseudogene. Structural analyses identified 118 simple sequence repeats (SSRs), 18 tandem repeats, and 191 dispersed repeats distributed throughout the mitochondrial genome. RNA editing prediction revealed 394 putative editing sites, with notable enrichment in NADH dehydrogenase genes. Critical modifications included start codon conversion in atp6 (ACG → AUG) and stop codon alterations in ccmFc (CGA → UGA) and rpl16 (UAG → UAA). Comparative genomic analyses detected 50 chloroplast-derived DNA fragments, constituting 6.0% of the mitogenome, indicative of historical plastid-to-mitochondrion transfer events. Codon usage bias analysis demonstrated phenylalanine (Phe) as the most frequently encoded amino acid, with selection pressure identified as the predominant driver of codon usage patterns. Phylogenetic reconstruction employing 22 conserved PCGs resolved intra-ordinal relationships among eight Malpighiales families, revealing Phyllanthaceae sister to Salicaceae with robust nodal support. This study advances the utilization of mitochondrial genomes for elucidating phylogenetic relationships within Phyllanthus while providing essential genomic resources for future comparative mitogenomic investigations in Phyllanthaceae. The structural complexity revealed through repeat analyses and RNA editing patterns offers novel insights into plant mitochondrial genome evolution.