Genetica最新文献

{"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":"https://doi.org/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_ST 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":1.3,"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}

{"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":"https://doi.org/10.1007/s10709-026-00266-7","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":1.3,"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}

{"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":1.3,"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}

{"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":"https://doi.org/10.1007/s10709-026-00265-8","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":1.3,"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}

{"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":"https://doi.org/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":1.3,"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}

{"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":"https://doi.org/10.1007/s10709-026-00264-9","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"13"},"PeriodicalIF":1.3,"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}

{"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":"https://doi.org/10.1007/s10709-026-00260-z","url":null,"abstract":"<p><p>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.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"11"},"PeriodicalIF":1.3,"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}

{"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":"https://doi.org/10.1007/s10709-026-00262-x","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"10"},"PeriodicalIF":1.3,"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}

{"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":1.3,"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}

{"title":"Genome-wide identification and expression analysis of the monosaccharide transporter (MST) gene family in response to exogenous sugar in wheat (Triticum aestivum L.).","authors":"Jun Zhang, Bo Zhang, Shuang Zhou, Wenzhong Tian, Rong Zhang, Yiren Chen, Binbin Guo, Chao Ma","doi":"10.1007/s10709-026-00257-8","DOIUrl":"https://doi.org/10.1007/s10709-026-00257-8","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":"8"},"PeriodicalIF":1.3,"publicationDate":"2026-01-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"146013220","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}