{"title":"Molecular evolution and antigenic mapping of classical swine fever virus: a comprehensive analysis of E2 genomic variability and selection dynamics.","authors":"Nagarajan Siddharthan, Sharanagouda S Patil, Vijay Muruganantham, Roopa Mahadevaswamy, Kuralayanapalya Puttahonnappa Suresh, Jagadish Hiremath, Shivasharanappa Nayakvadi","doi":"10.1007/s10709-026-00269-4","DOIUrl":"10.1007/s10709-026-00269-4","url":null,"abstract":"<p><p>Worldwide, the pig industry suffers financial losses due to the extremely contagious disease caused by the classical swine fever virus (CSFV). However, comprehensive and global genotyping information for CSFV remains scarce. A total of 1,053 full length E2 sequences of CSFV from the NCBI database were used in this study. According to phylogenetic analysis, the strains were grouped into dominant genetic subgroups. The positive selection pressures on the CSFV E2 envelope protein genes were also evaluated and a site-by-site examination of the dN/dS ratio was conducted to pinpoint certain codons that diversify under positive selection. Phylogenomic analyses using maximum likelihood (ML) and Bayesian inference (BI) confirmed that the 1,053 strains clustered within the previously defined five subgenotypes (1.1, 1.2, 2.1, 2.3 and 3.4). One positively selected site was identified at amino acid residue position 71. Bayesian coalescent analysis estimated an evolutionary rate of 1.364 × 10⁻³ substitutions per site per year (95% HPD: 1.1808 × 10⁻³-1.5602 × 10⁻³) and a tMRCA of approximately 1816 (95% HPD: 1796-1837). The effective population size of CSFV began increasing in the 1920s, continued to rise until the 1950s, and then remained stable thereafter. Sequence-based antigenic mapping was used to evaluate antigenic relationships among CSFV strains, revealing that most strains clustered closely together. Understanding the molecular epidemiology and functional significance of positively selected amino acid sites may aid in predicting changes in virulence and inform vaccine development and disease control strategies.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-05-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147876738","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-04-26DOI: 10.1007/s10709-026-00267-6
Bhuvadol Gomontean, Wannachai Wannasingha, Khamla Inkhavilay, Chavanut Jaroenchaiwattanachote, Peter H Adler, Pairot Pramual
{"title":"Population genetics of the black fly Simulium asakoae from Laos and its relationships with Southeast Asian populations.","authors":"Bhuvadol Gomontean, Wannachai Wannasingha, Khamla Inkhavilay, Chavanut Jaroenchaiwattanachote, Peter H Adler, Pairot Pramual","doi":"10.1007/s10709-026-00267-6","DOIUrl":"10.1007/s10709-026-00267-6","url":null,"abstract":"<p><p>Simulium asakoae is a widespread species of black fly in Southeast Asia and a potential vector of parasites of medical and veterinary importance. Despite its broad distribution and diverse habitats, population genetic information remains limited. We investigated the genetic diversity, population structure, and demographic history of S. asakoae in Laos and examined its genetic relationships with populations from other Southeast Asian countries, using mitochondrial cytochrome c oxidase subunit I (COI) sequences. A total of 369 COI sequences (241 generated in the present study and 128 retrieved from GenBank) were analyzed. Of these, 284 sequences (241 from this study and 43 from GenBank) originated from nine locations across five provinces in Laos. Among the Laotian specimens, 51 haplotypes were identified, showing high haplotype diversity (Hd = 0.9063) and moderate nucleotide diversity (π = 0.0080). Intraspecific genetic divergence among Lao populations ranged from 0 to 2.49%, increasing slightly to 2.66% when regional sequences were included. Median-joining network analyses revealed no major genetic breaks or clear geographic structuring in Laos or across Southeast Asia, indicating extensive gene flow. Pairwise F<sub>ST</sub> analyses, however, detected significant differentiation among some populations. Demographic analyses, including mismatch distributions and neutrality tests, supported a scenario of recent population expansion, with estimated expansion times of approximately 13,000 years ago for Lao populations and 15,000 years ago at the regional scale. These timeframes coincide with the transition from the cool dry Pleistocene to the warm humid Holocene, which might have facilitated population growth and range expansion. Our results demonstrate that S. asakoae forms a genetically diverse, weakly structured, and well-connected metapopulation across Laos and Southeast Asia. This extensive connectivity might enhance the ability of this species to maintain and disseminate parasites, indicating the importance of regional-scale surveillance and future studies incorporating nuclear markers and ecological data.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147789481","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-04-11DOI: 10.1007/s10709-026-00266-7
Claudia Corbi-Botto, María E Zappa, Sebastián A Sadaba, Pilar Peral-García, Guillermo Giovambattista, Silvina Díaz
{"title":"Genetic diversity in the Criollo Argentino horse from SNP array data.","authors":"Claudia Corbi-Botto, María E Zappa, Sebastián A Sadaba, Pilar Peral-García, Guillermo Giovambattista, Silvina Díaz","doi":"10.1007/s10709-026-00266-7","DOIUrl":"10.1007/s10709-026-00266-7","url":null,"abstract":"<p><p>The Criollo Argentino horse is a national symbol and a heritage breed that represents both cultural identity and a key component of traditional production systems in Argentina. This study aimed to assess the genetic differentiation of the Criollo Argentino relative to other horse breeds and to infer potential factors shaping its diversity through the genomic analysis of 24 representative animals. Samples were genotyped using a medium-density SNP array containing 65,157 markers, and genetic diversity analyses were conducted across autosomal SNP sets filtered under different criteria. Contemporary effective population size was estimated using both linkage disequilibrium from SNP data (Ne = 155.6) and pedigree analysis (fe = 157.7), showing remarkable consistency between genomic and genealogical approaches. Measures of expected heterozygosity, Hardy–Weinberg equilibrium, and linkage disequilibrium showed that Criollo Argentino horses retain moderate to high levels of genetic variability. Results further revealed that the Criollo Argentino is a genetically well-defined population with high within-individual diversity and clear differentiation from other breeds. In addition, the Criollo Argentino population was compared with eight other horse breeds to evaluate genetic distance and population structure. Estimates of genetic distance, population structure, and fixation index values were consistent with the documented history and development of the breed, while PCA and Bayesian clustering analyses supported a shared origin between the Criollo Argentino and the Peruvian Paso, both derived from Iberian horses introduced to the Americas during colonization. Overall, this work provides genomic evidence that strengthens the historical and biological characterization of the Criollo Argentino and supports informed decision-making for breeding, management, genetic improvement, and conservation programs for the breed.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147663519","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-03-04DOI: 10.1007/s10709-025-00256-1
Yasuko Kato, Raito Minami, Mai Sano, Kazushi Miyatake, Aki Yamamoto, Hitomi Nakazawa, Nobuyuki Inomata, Ian A Boussy, Masanobu Itoh
{"title":"Artificial competition shows the replicative superiority of KP elements over complete P elements in Drosophila melanogaster and D. simulans.","authors":"Yasuko Kato, Raito Minami, Mai Sano, Kazushi Miyatake, Aki Yamamoto, Hitomi Nakazawa, Nobuyuki Inomata, Ian A Boussy, Masanobu Itoh","doi":"10.1007/s10709-025-00256-1","DOIUrl":"10.1007/s10709-025-00256-1","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147357511","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-03-04DOI: 10.1007/s10709-026-00265-8
M Manjunath, C S Damini, V Shakunthala
{"title":"Cis-regulatory divergence and misexpression of spermatogenesis genes underlie hybrid male sterility in the Drosophila bipectinata species complex.","authors":"M Manjunath, C S Damini, V Shakunthala","doi":"10.1007/s10709-026-00265-8","DOIUrl":"10.1007/s10709-026-00265-8","url":null,"abstract":"<p><p>Hybrid male sterility (HMS) is one of the most common and earliest forms of postzygotic reproductive isolation in Drosophila, often arising from defects in spermatogenesis linked to regulatory divergence of rapidly evolving male-biased genes. The Drosophila bipectinata species complex (D. bipectinata, D. malerkotliana, D. parabipectinata, and D. pseudoananassae) provides a valuable system to study the speciation paradigm, since, all the twelve F₁ hybrid males are sterile, the precise stage of spermatogenic failure differs among crosses. Here, we integrate cytological, transcriptional, and regulatory sequence analyses to examine the basis of sterility in this sub-complex. Cytological assays revealed that hybrid testes exhibit developmental arrest at different spermatogenesis stages, covering from reduced primary spermatocytes to absence of individualized sperm. Quantitative RT-PCR of seven spermatogenesis genes—aly, bam, sa, dj, topi, can, and Mst98Ca—showed significant downregulation among hybrid males relative to parental species, linking transcriptional misregulation with observed phenotypic defects in spermatogenesis. To test whether regulatory divergence underlies this misexpression, we analyzed ~ 1–2 kb promoter regions of five genes (aly, bam, sa, dj, and topi). Motif scans using FIMO identified several lineage-specific turnover of transcription factor binding sites, also PWM-delta analysis revealed substantial interspecific differences in predicted binding strength for many key testis transcription factors. These results demonstrate that HMS in the D. bipectinata complex is consistently associated with spermatogenic arrest and misregulation of genes essential for germline proliferation, meiotic progression, and spermiogenesis. The concordance between expression changes and promoter divergence supports a role for cis-regulatory evolution in hybrid dysfunction, while also leaving open the contribution of trans-acting factors. This study situates the D. bipectinata complex within the broader framework of Drosophila hybrid sterility, extending and highlighting the evolutionary sensitivity of spermatogenesis and regulatory divergence in speciation.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147357549","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-02-18DOI: 10.1007/s10709-026-00263-w
Swarup Das, Subhajit Ghosh, Subarna Thakur
{"title":"Comprehensive computational insights into Plasmodium retrocopies reveals potential roles in virulence-associated functions.","authors":"Swarup Das, Subhajit Ghosh, Subarna Thakur","doi":"10.1007/s10709-026-00263-w","DOIUrl":"10.1007/s10709-026-00263-w","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"12"},"PeriodicalIF":2.0,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222221","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-02-18DOI: 10.1007/s10709-026-00264-9
Diego O Urquía, Sten Anslan, Leho Tedersoo, Sebastian A Espinoza-Ulloa, Miguel Vences, Diego Páez-Rosas
{"title":"Complete mitogenomes of the endangered Galapagos fur seal (Arctocephalus galapagoensis): new insights on its evolutionary history.","authors":"Diego O Urquía, Sten Anslan, Leho Tedersoo, Sebastian A Espinoza-Ulloa, Miguel Vences, Diego Páez-Rosas","doi":"10.1007/s10709-026-00264-9","DOIUrl":"10.1007/s10709-026-00264-9","url":null,"abstract":"<p><p>Of the two otariid species endemic to the Galapagos Islands, the Galapagos fur seal (GFS, Arctocephalus galapagoensis) remains the least studied due to its remote distribution restricted to the western islands of the archipelago, a region uniquely influenced by the cold, productive Equatorial Undercurrent (EUC). This study presents the first two complete GFS mitogenomes, assembled from scat samples collected at the Cabo Douglas rookery on Fernandina Island, to contribute to elucidating the evolutionary history of this endangered species. Time-calibrated phylogenies indicate most Arctocephalus species form a monophyletic group. These also show GFS as sister to South American and New Zealand fur seals, diverging 1.91–1.68 MYA (million years ago). This divergence coincides with the early Pleistocene cooling (Gelasian–Calabrian transition), when colder oceans favored otariid dispersal, thus suggesting the time of arrival of fur seals to the Galapagos Islands. The Galapagos region, maintained by the EUC, likely served as a climate refugium enabling fur seal persistence in tropical waters despite later interglacial warming. This study underscores the utility of non-invasive genetic sampling and highlights the role of the Galapagos marine ecosystem as a climate refugia for biodiversity in the face of oceanic warming.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"13"},"PeriodicalIF":2.0,"publicationDate":"2026-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146222280","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-02-12DOI: 10.1007/s10709-026-00260-z
Muhammad Mudasir, Muhammad Shahzad, Ayesha Bibi, Shareef Gul, Liu Qiuyi, Sarmad Frogh Arshad, Hameed Gul, Ali Shahzad
{"title":"Genome-wide identification and expression analysis of YTH gene family in barley reveals their potential role under abiotic stresses.","authors":"Muhammad Mudasir, Muhammad Shahzad, Ayesha Bibi, Shareef Gul, Liu Qiuyi, Sarmad Frogh Arshad, Hameed Gul, Ali Shahzad","doi":"10.1007/s10709-026-00260-z","DOIUrl":"10.1007/s10709-026-00260-z","url":null,"abstract":"<p><p>N6-methyladenosine (m<sup>6</sup>A) 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 m<sup>6</sup>A-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 m<sup>6</sup>A 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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"11"},"PeriodicalIF":2.0,"publicationDate":"2026-02-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146168053","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-02-04DOI: 10.1007/s10709-026-00262-x
Samarth Sharma, Neha Thakur, Siddharth Tiwari, Jaspreet K Sembi
{"title":"Genome-wide study of Protein Arginine Methyltransferases (PRMT) gene family in selected orchid species: the epigenetic architects of orchid genome.","authors":"Samarth Sharma, Neha Thakur, Siddharth Tiwari, Jaspreet K Sembi","doi":"10.1007/s10709-026-00262-x","DOIUrl":"10.1007/s10709-026-00262-x","url":null,"abstract":"<p><p>Protein arginine methyltransferases (PRMTs) are an important group of epigenetic regulators that mediate methylation of target proteins at arginine residues. These post-translational histone modifiers play a substantial role in controlling various biological activities of plants by altering the chromatin structure and thus, regulating the gene expression. In the present study, a total of 24 putative PRMT genes were reported in three orchid species, Apostasia shenzhenica (eight AshPRMTs), Dendrobium catenatum (eight DcaPRMTs) and Phalaenopsis equestris (eight PeqPRMTs). Based on the presence of characteristic domains and conserved motifs, the PRMTs could be classified into three distinct types, type I, II and III which was substantiated using multiple sequence alignment. Phylogenetic analysis showed the distinct clustering of PRMTs into three types along with their PRMT counterparts of Arabidopsis thaliana and Oryza sativa. Prediction of secondary and tertiary protein structures as well as gene structures provided further validation of this classification. Furthermore, expression profiling across different vegetative and reproductive tissues and analysis of cis-regulatory promoter elements suggested their plausible roles in various growth and development related processes. Since PRMT gene family constitutes an important class of histone-modifying enzymes playing a pivotal role in many morphological processes, this study would be an important base for functional validation of their role in important biological phenomenon in orchids.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"10"},"PeriodicalIF":2.0,"publicationDate":"2026-02-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146121155","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
GeneticaPub Date : 2026-02-01DOI: 10.1007/s10709-026-00261-y
Maryam Mehdizadeh Hakkak, Masoud Tohidfar
{"title":"Identifying a conserved transcriptional signature of drought and salt stress in Arabidopsis thaliana through meta-analysis, consensus network analysis, and deep learning.","authors":"Maryam Mehdizadeh Hakkak, Masoud Tohidfar","doi":"10.1007/s10709-026-00261-y","DOIUrl":"10.1007/s10709-026-00261-y","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"9"},"PeriodicalIF":2.0,"publicationDate":"2026-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146101090","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}