Genetica最新文献

{"title":"Genetic diversity and phylogenetic placement of the Procapra picticaudata (Tibetan gazelle) from northern Sikkim, India.","authors":"Deepesh Saini, Gaurav Sonker, Pooja Pant, Divyanshi Bisht, Vishnupriya Kolipakam, Sandeep Tambe, Sambandam Sathyakumar, Sandeep Kumar Gupta","doi":"10.1007/s10709-026-00298-z","DOIUrl":"https://doi.org/10.1007/s10709-026-00298-z","url":null,"abstract":"<p><p>We analysed mitochondrial control region sequences of Procapra picticaudata (Tibetan gazelle) in northern Sikkim, India, to assess its genetic diversity, phylogenetic relationship, and demographic history. We identified 12 haplotypes from 24 successfully amplified fecal samples, exhibiting high haplotype diversity (h = 0.916) and nucleotide diversity (π = 0.00627). Bayesian phylogenetic analyses revealed that Sikkim haplotypes did not form a geographically exclusive clade; instead, they clustered with Tibetan Plateau haplotypes, whereas Chinese mountain samples formed a distinct lineage. Considerable genetic distance was observed between Indian and Chinese P. picticaudata and P. przewalskii. The newly generated sequences provide baseline information for future range-wide population genetic assessments and conservation planning for this small peripheral population.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149197895","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":"Unlocking mitogenomic analysis of Bagroides melapterus Bleeker, 1851 (Siluriformes: Bagridae) from Borneo: characterization and the placement within bagrids phylogeny.","authors":"Muhammad Hilman Fu'adil Amin, Rahmat Hidayat, Lariman, Darmawan Setia Budi, Suciyono, Gde Raka Angga Kartika, Shantanu Kundu, Hyun-Woo Kim, Nur Indradewi Oktavitri","doi":"10.1007/s10709-026-00297-0","DOIUrl":"https://doi.org/10.1007/s10709-026-00297-0","url":null,"abstract":"<p><p>The family Bagridae comprises a diverse group of freshwater catfishes distributed throughout Asia and Africa; however, several genera remain poorly represented in genomic studies. Among them, the monotypic genus Bagroides has lacked complete mitochondrial genomic data, limiting our understanding of its evolutionary history and phylogenetic position. Here, we report the first complete mitochondrial genome of Bagroides melapterus, providing the inaugural mitogenomic resource for the genus. The complete mitogenome of B. melapterus, a circular molecule of 16,542 bp with a GC content of 43.6%, was sequenced and characterized to elucidate its genetic composition and phylogenetic position. The mitogenome comprises 37 genes, including 13 protein-coding genes (PCGs), 22 transfer RNAs, 2 ribosomal RNAs, and a control region. Comparative analyses revealed a conserved genomic organization consistent with other members of Bagridae. To resolve its evolutionary placement, phylogenetic relationships were reconstructed using concatenated nucleotide sequences of the 13 mitochondrial PCGs and two rRNAs from representative bagrid taxa under Maximum Likelihood and Bayesian Inference frameworks, followed by divergence time estimation using a relaxed molecular clock. Both phylogenetic approaches recovered highly congruent topologies, consistently placing B. melapterus as the sister lineage of Pseudomystus siamensis with strong statistical support. Time-calibrated analyses indicated that these lineages diverged approximately 20.52 million years ago (mya) during the early Miocene, whereas the Sundaic Bagroides-Pseudomystus lineage separated from the common ancestor of the Tachysurus lineage around 44.89 mya in the mid Eocene. These divergence events coincide with major paleogeographic and climatic changes that likely contributed to the diversification of Southeast Asian freshwater fishes. As the first complete mitochondrial genome of Bagroides, this study fills a critical gap in the mitogenomic resources of Bagridae, refines the phylogenetic framework of the family, and provides an essential genomic foundation for future systematic, phylogenomic, and conservation studies of Asian freshwater catfishes.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149167666","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":"In Memoriam: Pierre Capy and Ronny C. Woodruff.","authors":"Juan L Bouzat, Horacio Naveira","doi":"10.1007/s10709-026-00294-3","DOIUrl":"https://doi.org/10.1007/s10709-026-00294-3","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149139486","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 and conservation of a rare Miconia species (Melastomataceae) from the Brazilian Atlantic Forest.","authors":"Gabriela Goebel, Ana Flávia Augustin, Eduardo Koerich Nery, Yohan Fritsche, Valdir Marcos Stefenon, Duane Fernandes Lima, Mayara Krasinski Caddah","doi":"10.1007/s10709-026-00296-1","DOIUrl":"https://doi.org/10.1007/s10709-026-00296-1","url":null,"abstract":"<p><p>Biodiversity is undergoing an unprecedented global decline, and genetic diversity plays a fundamental role in ensuring species persistence. Miconia ulei, an endemic species from the eastern Atlantic Forest in Santa Catarina, southern Brazil, is rare and has few known populations. We investigated genetic diversity and population structure using microsatellite markers and assessed its conservation status following IUCN guidelines and by incorporating genetic parameters in the evaluation. Five extant populations were sampled across the species' known distribution, and twelve species-specific microsatellite markers were developed. Populations exhibited low to moderate levels of genetic diversity. Genetic differentiation among populations was generally low, although one population showed a distinct genetic structure. No isolation by distance was detected, suggesting that factors other than geographic distance may influence patterns of gene flow. Evidence of historical reductions in population size was detected in most populations. Together, these findings indicate that M. ulei has limited genetic variation and small, fragmented populations, increasing its vulnerability to future genetic loss. Our results support the need for conservation actions, including the formal inclusion of M. ulei in official Red Lists and the maintenance of habitat connectivity to promote long-term population persistence. As the first population genetic assessment of M. ulei, this study provides an important baseline for conservation planning and highlights the need for conservation genetic studies of other rare Atlantic Forest species.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13630976/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118955","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparative mitogenomics of six Thrips species reveals conserved architecture, repeat variation, and nucleotide composition bias.","authors":"Kamel A Saleh, Yagna B Adhyaru, Kethirisetty Nikhila, J Gowrishankar, Ali Khatibi, Sarbeswara Hota, S Murugan, Gaurav Raj, Sumit Sharma","doi":"10.1007/s10709-026-00295-2","DOIUrl":"10.1007/s10709-026-00295-2","url":null,"abstract":"<p><p>Thrips are widely distributed insects with economic importance, but their evolutionary dynamics of the mitochondrial genome remain poorly understood. This study presented a computational mitogenomic analysis of six Thrips species obtained from a public repository. An analysis was performed to investigate patterns of genomic architecture and evolutionary variations. Mitochondrial genomes were analyzed using bioinformatic approaches, including annotation, syntenic comparison, gene content analysis, and SSR identification. Codon usage bias was measured using RSCU and CAI metrics, while skewness in nucleotide composition was studied using AT and GC skew analyses. Results suggest that there is generally a conservation of mitochondrial genome organization among the different species, but only limited rearrangements occur, and these are mainly associated with tRNA and non-coding sequences. The presence or absence of genes in Thrips was verified by re-annotation with MITOS2, followed by confirmation in the feature table in GenBank. SSR analysis showed few notable interspecific variability, where T. palmi and T. hawaiiensis seemed to have higher motif diversity and density, sort of. Codon usage patterns looked like they had a strong bias towards A/T-ending codons, and the CAI values suggested different levels of codon usage adaptation across species, using reference sets that were built from the mitochondrial protein-coding genes themselves. Also, we consistently observed positive AT-skew and negative GC-skew across all genomes, with more pronounced asymmetry in T. palmi and T. hawaiiensis. Overall, this work points to both conserved traits and lineage-specific features in Thrips mitochondrial genomes, giving some clues about their evolutionary dynamics while also broadening our understanding of insect mitochondrial genome evolution.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149118916","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":"Integrating evolutionary signals and predicted protein structure reveals localized molecular divergence in Cereus lineages.","authors":"Danilo T Amaral, João Alfredo Teodo, Maria Izadora Oliveira Cardoso, Evandro Marsola Moraes, Fernando Faria Franco, Isabel A S Bonatelli","doi":"10.1007/s10709-026-00293-4","DOIUrl":"10.1007/s10709-026-00293-4","url":null,"abstract":"<p><p>Understanding how positive selection shapes molecular evolution at the protein level remains a major challenge, particularly in non-model species. Here, we integrated phylogenetic evidence from candidate genes evolving under lineage-specific positive selection with comparative structural and biophysical analyses to investigate patterns of molecular divergence in the Cereus fernambucensis-C. insularis clade, which occupies contrasting island and continental environments. Based on a previous branch-site analysis, five orthogroups were selected for downstream analyses. Orthologous protein structures were predicted and compared, variability hotspots were identified, pockets proximity were evaluated, and the stability effects of lineage-specific substitutions were estimated. Across orthogroups, global folds were largely conserved, whereas molecular divergence was primarily associated with localized structural variation in flexible loops and surface-exposed regions. Variability hotspots were significantly enriched near predicted cavities in several orthogroups, indicating that molecular diversification was concentrated in structurally permissive regions frequently associated with putative interaction surfaces. Stability analyses of reconstructed branch-specific substitutions revealed heterogeneous energetic effects, ranging from stabilizing to strongly destabilizing changes, while global protein architecture remained largely conserved. Together, these results suggest that evolutionary divergence in Cereus lineages is primarily associated with localized modifications of surface-accessible regions rather than large-scale structural innovation. More broadly, our findings demonstrate how integrating molecular evolutionary analyses with structural bioinformatics provides a robust framework for interpreting candidate adaptive genes in non-model organisms, while highlighting both the potential and limitations of structure-informed evolutionary inference.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13615019/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066071","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular phylogenetics, distribution and evolution of the TPP riboswitch.","authors":"Dimitrios Kaloudas, Nikolet Pavlova, Martina Traykovska, Robert Penchovsky","doi":"10.1007/s10709-026-00292-5","DOIUrl":"10.1007/s10709-026-00292-5","url":null,"abstract":"<p><p>Thiamine pyrophosphate (TPP) riboswitches are the only riboswitch class identified in eukaryotes. They therefore provide a unique model for reconstructing the evolution of RNA-based gene regulation across life's domains. We investigated the molecular evolution, structural diversification, and genomic-context reassignment of the TPP riboswitch across archaea, bacteria, cyanobacteria, fungi, algae, and land plants using phylogenetic reconstruction, covariance-model-guided sequence analysis, comparative secondary-structure analysis, genomic-context annotation, and covariation-based inference. Our analyses establish an early prokaryotic origin of the TPP riboswitch as a 5'- UTR-associated regulatory element. Archaea retain the most compact ancestral scaffold. The transition to bacteria is characterized by extensive compensatory evolution. Bacteria preserve the canonical fold but exhibit the strongest covariation. Within bacteria, cyanobacteria exhibit a reduced architecture while retaining a conserved ligand-binding core, indicating an early reform event. Methylogaea oryzae branches within the cyanobacterial clade, identifying horizontal acquisition of a thiC-TPP riboswitch cassette. The transition into the green lineage is marked by the repositioning of the riboswitch from the ancestral 5'-UTR to the 3'-UTR. This architecture is found in the charophyte Closterium, indicating that the plant-type 3'-UTR state predates land plants. Fungi retain mainly 5'-UTR organization but also contain a distinct 3'-UTR NMT1/thi5-associated clade, defining a second eukaryotic regulatory configuration derived through horizontal transfer from early green lineages. These results suggest a continuous evolutionary trajectory of the TPP riboswitch from an ancestral prokaryotic 5'-UTR regulator to the green-lineage repositioning of the 3'-UTR, to fungal functional reassignment, and the secondary emergence of an alternative 3'-UTR state.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149066161","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":"The complete mitochondrial genome of Malaysian Macrobrachium rosenbergii (De Man, 1879) and its phylogenetic relationship among Palaemonidae.","authors":"Siti Amalia Aisyah Abdul-Halim, Dania Aziz, Fadhil Syukri, Yuzine Esa","doi":"10.1007/s10709-026-00291-6","DOIUrl":"10.1007/s10709-026-00291-6","url":null,"abstract":"<p><p>The giant freshwater prawn (Macrobrachium rosenbergii) is an economically important aquaculture species in Southeast Asia. Despite its significance, complete mitochondrial genome data from Malaysian populations remain scarce, limiting insights into genetic variation and phylogenetic relationships. This study aimed to sequence and characterized the complete mitochondrial genome of M. rosenbergii from Perak, Malaysia, and to assess its phylogenetic position relative to other regional populations. Genomic DNA was extracted and sequenced using next-generation sequencing. The mitochondrial genome was assembled, annotated, and its nucleotide composition and gene arrangement were analyzed. Phylogenetic analysis was performed using Maximum Likelihood method based on the 13 mitochondrial protein-coding genes of representative Palaemonidae species. The circular mitochondrial genome of M. rosenbergii was 15,332 bp in length, comprised by 13 protein-coding genes, 22 tRNA genes, and two rRNA genes. Most genes were encoded on the heavy strand, with several located on the light strand, consistent with other crustaceans. The nucleotide composition exhibited an A + T bias. Phylogenetic analysis placed the Perak specimen in a strongly supported M. rosenbergii clade, confirming its identity and monophyly. Minor sequence divergence from previously reported mitogenomes was observed; however, given that this study is based on a single individual, these differences should be interpreted cautiously and do not allow inference of population-level differentiation. This mitogenome represents a valuable genetic resource for M. rosenbergii, supporting applications in aquaculture breeding programs, population genetics, and functional genomics. It also provides a reference for transcriptomic studies, enabling mitochondrial gene expression profiling and functional annotation.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-09-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"149018873","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":"Mitochondrial genome and phylogenetic analysis of Aster Indicus L.","authors":"Ying Meng, Yuting Liang, Kaiyue Wang, Youjuan Zhu, Xinxin Zhao, Tong Zhang, Jingyu Yang, Fei Han, Juan Wang, Jiangtao Wu, Xiaofeng Shen","doi":"10.1007/s10709-026-00290-7","DOIUrl":"10.1007/s10709-026-00290-7","url":null,"abstract":"<p><p>Aster indicus L. is a medicinally important species with therapeutic value from its entire plant. However, genomic research, particularly concerning the mitochondrial genome, remains sparse. This study sequenced the mitochondrial genome of A. indicus, revealing a length of 224,973 bp with an A/T content of 54.5%. The mitogenome encodes 54 protein-coding genes, 21 tRNAs, and 3 rRNAs. Identification of genomic features included 20 simple sequence repeats, 143 dispersed repeats, 15 tandem repeats, and 10 segments derived from chloroplast DNA. Analysis of codon usage indicated a preference for A/U-terminating codons. Comparative synteny analysis with 11 species in Asteraceae showed a 94.77% sequence identity with Aster batangensis Bureau & Franch., accompanied by extensive genomic rearrangements. Most protein-coding genes exhibited evidence of purifying selection, with the exception of nad1. Phylogenetically, A. indicus is closest to A. batangensis; as expected, the genus Aster is genetically closer to the genus Erigeron, in agreement with their placement in tribe Astereae, but distant from Arctium and Carthamus, that belongs to tribe Cardueae. This study delineates the structural characteristics and sequence features of the A. indicus mitochondrial genome and enriches the genetic resources of the genus Aster and Asteraceae family, and establishing a foundational basis for future functional, evolutionary, and pharmacological investigations of this therapeutically significant species.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148834818","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":"Integrating microsatellite data via locus-specific mode-shift harmonisation reveals circumpolar population structure in reindeer and caribou (Rangifer tarandus).","authors":"Magdalena Semina, Gulnara Svishcheva, Anna Kuznetsova, Danila Kozyrenko, Kasim Laishev, Yuri Stolpovsky","doi":"10.1007/s10709-026-00288-1","DOIUrl":"10.1007/s10709-026-00288-1","url":null,"abstract":"<p><p>Reindeer and caribou (Rangifer tarandus) occupy a vast northern range spanning Eurasia and North America, where understanding population structure is essential for conservation and management. However, comparative analyses across this circumpolar distribution are hindered by systematic allele-size offsets introduced by differences in genotyping platforms, laboratory protocols, and allele-calling procedures. Here, we applied a locus-specific mode-shift harmonisation procedure to integrate legacy microsatellite datasets from Alaska, Canada, and Russia. The final harmonised dataset included 1544 individuals from 42 populations genotyped at nine shared microsatellite loci. The procedure used dataset- and locus-specific modal allele differences to reduce systematic allele-size offsets while preserving within-dataset allele-frequency structure and heterozygosity status. To evaluate robustness, we compared diversity statistics before and after harmonisation, tested alternative reference alignments, and performed sensitivity analyses excluding populations with small sample sizes and loci with large modal allele shifts. We also assessed a pooled small-sample dataset in which sparsely represented populations were grouped within biologically meaningful regional or ecological units. Diversity estimates remained unchanged after harmonisation, as expected for constant locus-specific allele-size shifts, and broad interregional structure was retained across reference alignments and sensitivity filters. After harmonisation, PCA, DAPC, Nei-distance analysis, pairwise FST, and exploratory ADMIXTURE analyses consistently supported broad differentiation among Russian, Canadian, and Alaskan populations, with Alaskan populations occupying an intermediate position between Canadian and Russian groups. These results are consistent with historical connectivity across the Beringian region. Our study shows that reference-based mode-shift harmonisation can provide a practical framework for improving the comparability of heterogeneous microsatellite datasets when shared reference samples are unavailable, while remaining complementary to direct cross-laboratory calibration approaches.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"154 1","pages":""},"PeriodicalIF":2.0,"publicationDate":"2026-08-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"148834802","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}