Genetica最新文献

{"title":"Differential DNA methylation in response to host environment changes in Drosophila gouveai.","authors":"Adriano S Santos, Ester S Ramos, Vera L S Valente, Maura H Manfrin","doi":"10.1007/s10709-025-00230-x","DOIUrl":"10.1007/s10709-025-00230-x","url":null,"abstract":"<p><p>Organisms with a single genotype can express different phenotypes in response to rapid environmental changes, an event known as phenotypic plasticity, although the molecular basis is poorly understood. Epigenetic modifications mediate genotype-to-phenotype transitions and are related to phenotypic plasticity. Drosophila gouveai, a cactophilic species found in South America, exhibits morphological changes and differential methylation in its genome during the development; however the phenotypic plasticity is not yet elucidated. In this study, we investigated changes in genomic DNA methylation profiles and molecular targets when D. gouveai develops in Cereus hildmaniannus tissues or P. machrisii cactus. We assessed DNA methylation patterns using the MSAP technique, followed by direct sequencing. Our results indicate that internal methylation (target-CmCGG/CCmGG) comprises 33 loci in the genome in ovarian tissues in flies raised on C. hildmaniannus and 31 loci in flies raised on P. machrisii. In the trials of male flies, we found 42 methylated loci in flies developed on C. hildmaniannus and 21 loci in flies raised on P. machrisii. Epigenetic heterogeneity was observed between D. gouveai ovarian and testicular tissues. Additionally, the Galileo transposon element (TE) is targeted for methylation when flies develop on C. hildmaniannus. Methylation of transposable elements is known to play a role in genome stability. In conclusion, our data suggest that differential methylation occurs in the D. gouveai genome when using different cactus hosts.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"14"},"PeriodicalIF":1.3,"publicationDate":"2025-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143582405","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":"New insights into the adaptation mechanism of Cardisoma armatum hepatopancreas in the terrestrial environment by transcriptome analysis.","authors":"Zhengfei Wang, Sijia Hao, Chenchen Shen, Jinghao Hu, Yayun Guan, Zhuofan Chen, Shang Zhu, Xinyu Wang, Lv Wu","doi":"10.1007/s10709-025-00229-4","DOIUrl":"https://doi.org/10.1007/s10709-025-00229-4","url":null,"abstract":"<p><p>As a typical species of Gecarcinidae, Cardisoma armatum has adapted to the terrestrial environment. Meanwhile, C. armatum with unique living habits provides an excellent model for exploring the terrestrial adaptation mechanism of crabs. In this study, we have conducted a comprehensive transcriptomic analysis of C. armatum, aiming to deepen our understanding of the adaptive mechanisms operating within two groups: the air-exposed (AE) group and the water-immersed (WI) group, over eight hours. Genes that showed differential expression about adaptation to terrestrial environments were categorized into three groups: immune regulation, antioxidant system, and ion transport. The transcriptomic analysis also revealed a significant increase in the expression of genes related to immune response, antioxidant systems, and ion transport, such as the mitogen-activated protein kinase signaling pathway, tumor protein 53, superoxide dismutase 1, superoxide dismutase 2, solute carrier family 9 member A3, and Na⁺/K⁺/2Cl^- cotransporter, indicating that C. armatum responds positively to changes in habitat. This study aims to furnish a molecular rationale for the adaptive mechanisms that terrestrial and semi-terrestrial crab species exhibit in their terrestrial habitats, thereby contributing to a deeper understanding of their evolutionary adaptations.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"13"},"PeriodicalIF":1.3,"publicationDate":"2025-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143568966","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":"Comparative genetic analysis of pathogenic and attenuated strains of Junín virus.","authors":"Pablo Daniel Thomas, María Florencia Ferrer, Mauricio J Lozano, Ricardo Martín Gómez","doi":"10.1007/s10709-025-00228-5","DOIUrl":"https://doi.org/10.1007/s10709-025-00228-5","url":null,"abstract":"<p><p>Junín virus (JUNV) is a mammarenavirus that causes Argentine hemorrhagic fever (AHF). Mammarenaviruses are RNA viruses with an ambisense, bi-segmented genome containing four genes encoding the glycoproteins (GPC), the nucleoprotein (NP), the RNA polymerase (L) and the matrix protein (Z). Several JUNV strains with different pathogenicity have already been fully sequenced. We performed a comprehensive and comparative analysis of their genetic differences and phylogeny, focusing on the synonymous codon usage patterns of the JUNV proteins. We found a nucleotide identity of > 95% between strains, with significant differences between all genes for GC% and Z and L genes for GC3%. Analysis of relative synonymous codon usage showed that codons AGA and AGG of the amino acid arginine were overrepresented, while CGC, CGA and CGG of arginine, GCG of alanine, ACG of threonine, CCG of proline and TCG of serine were underrepresented in the GPC, NP and L genes. A weak codon usage bias was observed, with GPC having a significantly higher effective number of codons. Moreover, selection could explain at least 83% of the observed bias. Analysis of the codon adaptation index revealed a better adaptation for B cells and kidney and a lower one for endothelial cells. We also observed a possible reassortment event between the MC2 and Romero strains. This work provides a new perspective on the genetic diversity of JUNV strains, which may contribute to the development of new approaches for future research into the evolutionary model, origin and host adaptation of JUNV causing AHF.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"12"},"PeriodicalIF":1.3,"publicationDate":"2025-02-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143375035","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":"Drosophila telomeric protein Verrocchio is an ortholog of STN1.","authors":"Ion Udroiu, Antonella Sgura","doi":"10.1007/s10709-025-00226-7","DOIUrl":"https://doi.org/10.1007/s10709-025-00226-7","url":null,"abstract":"<p><p>In most Eukaryota, telomeres are protected by the CST complex, composed of CTC1, STN1 and TEN1. In Drosophila, instead, another complex is present, composed of Modigliani, Tea and Verrocchio. We performed a search for STN1 orthologs in Arthropoda, in order to verify if Verrocchio can be considered as such. We found that STN1 in Arthropoda is shorter than in other Metazoa and shares the same architecture with Verrocchio. Despite high sequence divergence between human and Drosophila, we have discovered that Verrocchio is an ortholog of STN1.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"11"},"PeriodicalIF":1.3,"publicationDate":"2025-01-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016775","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":"Comparative analysis of the WRKY gene family between Chimonanthus praecox and C. salicifolius.","authors":"Wei Zou, Gui-Ting Hu, Fang-Fang Gui, Xin-Chen He, Priyanka Borah, Li Zhu, Hui-Juan Ning, Li-Yuan Yang","doi":"10.1007/s10709-025-00227-6","DOIUrl":"https://doi.org/10.1007/s10709-025-00227-6","url":null,"abstract":"<p><p>Gene duplications provide evolutionary potentials for generating novel functions. Chimonanthus praecox and C. salicifolius are closely related species from Calycantaceae, Magnoliids. In this study, we compared the WRKY gene family from C. praecox and C. salicifolius, and predicted the potential gene function through gene expression patterns to explore the evolution of orthologous and paralogous gene pairs. A total of 73 and 85 WRKY genes were identified and analyzed from the whole genome sequencing of C. praecox and C. salicifolius. Based on the phylogenetic analysis, CpWRKY and CsWRKY genes were clustered into three groups (Group I、II、III) and 5 subgroups (Group IIa、IIb、IIc、IId、IIe). In C. praecox and C. salicifolius, we identified thirty-six and fifty-four pairs of WRKY segmental duplicated genes, respectively, along with two and three pairs of tandem duplicates, indicating that segmental duplication plays a crucial role in the evolution of Chimonanthus WRKY gene family. Most WRKY duplication gene pairs originated from segmental duplications before the first whole genome duplication (WGD), highlighting this period as a significant source of genetic diversity and functionality for the WRKY family. The analysis of WRKY gene expression levels suggests that CsWRKY18 and CsWRKY68 may promote the growth of the roots in C. salicifolius. Comparisons of expression profiles between species revealed that five orthologous gene pairs presented identical expression trends, indicating functional conservation and absence of neo-functionalization or sub-functionalization. However, most orthologous gene pairs exhibit differences in expression patterns, suggesting that they have undergone functional divergence. This functional differentiation may be due to the different selective pressures faced by C. praecox and C. salicifolius during their speciation processes. This study provided detailed information on the WRKY gene family from C. praecox and C. salicifolius, and a new insight for studying gene duplication and function evolution.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"10"},"PeriodicalIF":1.3,"publicationDate":"2025-01-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143016703","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":"Azotobacter biodiversity in Egypt using microbiological, biochemical, and molecular-biology multidisciplinary approach.","authors":"Ahmed M A Kenawy, Ahmed I Khalil, Bahy A Ali, Nehal M El-Deeb, Ahmed M Haddad","doi":"10.1007/s10709-024-00224-1","DOIUrl":"https://doi.org/10.1007/s10709-024-00224-1","url":null,"abstract":"<p><p>The presence of Azotobacter bacteria in the soil plays an important role in increasing its fertility and enhancing plant health. Azotobacter diversity depends on several environmental factors, particularly soil texture, pH, and nutrient content. The current study investigated the diversity of Azotobacter in various soil samples collected from 10 different governorates along the river Nile valley and its delta, Northern Mediterranean shore, Sinai, and Upper Egypt regions. The sampling sites spanned different environmental and ecological conditions of the Egyptian land either cultivated (agricultural land) or uncultivated (desert land). Fifty Azotobacter isolates were isolated and characterized based on cell morphology, culture properties, physiological, biochemical, and molecular characteristics. In addition, the alginate production capacity of the isolates was investigated. The results indicated that Egyptian soils are rich in Azotobacter diversity. The isolates were Gram-negative short rods, appearing either as single cells or in diploid structures. The isolates showed high variability in alginate production where two isolates (BH3 and AST4) were the highest alginate producers (3.12 and 4.22 g alginate L^- 1), respectively. 16S-rDNA sequencing and 16S-rDNA RFLP analyses indicated that despite the presence of Azotobacter salinestris and Azotobacter vinelandii in the Egyptian soil, Azotobacter chroococcum was the predominant species. In addition, sequence analysis of the gene coding for the transcription factor AlgU confirmed the results of 16S-rRNA gene sequence analysis. RAPD-REP and BOX-PCR were used to study the polymorphism among the isolates. High levels of microbial diversity were found using these DNA primers as 6-9 fingerprinting profiles were retrieved.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"9"},"PeriodicalIF":1.3,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142958976","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":"Impacts of habitat fragmentation on the genetic diversity of the endangered Guatemalan fir (Abies guatemalensis Rehder).","authors":"José Alejandro Ruiz-Chután, Marie Kalousová, Bohdan Lojka, Sofia Colocho-Hernández, José Pablo Prado-Córdova, Luis Montes, Amilcar Sánchez-Pérez, Julio Ernesto Berdúo-Sandoval","doi":"10.1007/s10709-024-00225-0","DOIUrl":"https://doi.org/10.1007/s10709-024-00225-0","url":null,"abstract":"<p><p>Abies guatemalensis Rehder, an endangered conifer endemic to Central American highlands, is ecologically vital in upper montane forests. It faces threats from habitat fragmentation, unsustainable logging, and illegal Christmas tree harvesting. While previous genetic studies on mature trees from eighteen populations showed high within-population diversity and limited among-population differentiation, the genetic impact of recent anthropogenic pressures on younger generations has yet to be discovered. Understanding these effects is crucial for developing effective conservation strategies for this vulnerable species. We sampled 170 young trees (< 15 years old) from seven populations across Guatemala. Seven microsatellite markers were used to analyse genetic diversity, population structure, and recent demographic history. Moderate levels of genetic diversity were observed within populations (mean Shannon diversity index = 4.97, mean Simpson's index = 0.51, mean allelic richness = 11.59, mean observed heterozygosity = 0.59). Although genetic structure broadly aligned with mountain corridors, substantial admixture patterns suggest historical connectivity across all populations. Most populations showed evidence of recent bottlenecks (p < 0.05) and inbreeding. The results suggest a potential decline in genetic diversity and increased population structuring (Φ_ST = 0.274, p < 0.01) over the past decades compared to the previous study on old trees. The observed genetic patterns indicate ongoing impacts of habitat fragmentation and anthropogenic pressures on A. guatemalensis. Conservation efforts should prioritise expanding effective population sizes and facilitating gene flow, particularly for isolated populations. While restoration efforts may be logistically easier within mountain ranges, genetic evidence suggests that increasing overall population connectivity could benefit this species. Management strategies should implement systematic seed collection protocols to maintain genetic diversity in future populations. These findings highlight the urgent need for conservation measures to preserve remaining genetic diversity and promote connectivity among A. guatemalensis populations.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"8"},"PeriodicalIF":1.3,"publicationDate":"2024-12-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142878525","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":"Effects of domesticated-to-wild gene flow on the genetic structure and diversity of wild papaya (Carica papaya L.) in its Mesoamerican diversity area.","authors":"Mauricio Heredia-Pech, Jaime Martínez-Castillo, Daniela A Martínez-Natarén, Pedro Ruiz-Gil, Mónica I Jiménez-Rojas, Matilde M Ortiz-García, Mariana Chávez-Pesqueira","doi":"10.1007/s10709-024-00223-2","DOIUrl":"https://doi.org/10.1007/s10709-024-00223-2","url":null,"abstract":"<p><p>Due to the increase in demand for food production worldwide, the cultivation of improved varieties is used as a strategy in order to maximize production. The improved Maradol papaya variety was introduced to the Yucatan Peninsula (YP), Mexico, the Mesoamerican diversity area of papaya, in the 1990s. The domesticated and wild papaya belong to the same species (Carica papaya L.), which promotes gene flow from crops to their wild relatives, threatening the genetic diversity of wild papaya populations in the region. In this study, we used a population genomic approach to evaluate the impact of domesticated-to-wild gene flow on the genetic structure and diversity of wild papaya in the YP. We used 2054 SNP markers for 227 wild individuals from 15 collection sites and 127 domesticated individuals from 13 Maradol papaya plantations. We found, (a) the presence of individuals that may be the result of a hybridization process between wild and domesticated papaya; (b) a higher genetic diversity in the wild group (H_E = 0.18) in comparison to the domesticated group (H_E = 0.09); and (c) low migration rates from domesticated to wild plants (m = 0.005). The domesticated-to-wild gene flow in C. papaya can have a negative effect on the genetic diversity and adaptive potential of wild populations from this region. The conservation of crop wild relatives should be a priority since they are part of various ecological processes and are considered natural reservoirs of genetic diversity for crops.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"7"},"PeriodicalIF":1.3,"publicationDate":"2024-12-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142814953","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 chloroplast genome characterization of three Plagiomnium species and the phylogeny of family Mniaceae.","authors":"Lan Huang, Jun Wen, M James C Crabbe, Chiqing Chen, Zhumei Ren","doi":"10.1007/s10709-024-00217-0","DOIUrl":"https://doi.org/10.1007/s10709-024-00217-0","url":null,"abstract":"<p><p>The taxonomic concepts and phylogenetic relations among genera of the family Mniaceae have given rise to much controversy in recent years, including Mnium, Plagiomnium, and Pohlia. Chloroplast genome study of these genera will be helpful to reflect the fact of this relationship. In this study, we sequenced three species in the Plagiomnium genus using an Illumina HiSeq 4000 platform. The complete chloroplast genomes of P. rostratum, P. succulentum and P. vesicatum were 125,196 bp, 124,689 bp, and 124,663 bp in length, which all contained a quadripartite structure including two copies of the invert repeats (IR, 10,120 bp, 9,818 bp, and 9,665 bp), one large single copy region (LSC, 86,395 bp, 86,299 bp, and 86,532 bp), and one single copy region (SSC, 18,561 bp, 18,754 bp, and 18,801 bp). The overall GC contents were 29.8%, 30.5%, and 30.5% respectively. The simple sequence repeats (SSRs) were detected in conjunction with Plagiomnium acutum, with variable sites genes observed: rpoC2, ycf1, and ycf2. Combined with the other three sequences published in Mniaceae, analyses of codon usage, repeats sequences, GC contents, and gene features revealed similarities among the seven species in Mniaceae. The trend of nucleotide diversity (Pi) in the seven complete chloroplast genomes showed Pi > 0.056: trnI-rpl23, petG-petL-psbE, trnK-chlB, trnG-trnR-atpA, rpoB-trnC-ycf66, ndhB, trnN-ndhF, and rps15-ycf1. We confirmed the phylogenetic relationships that Plagiomnium genus is a sister group with Mnium, while the Pohlia genus is not a monophyletic group. Phylogenetic analyses corroborated the monophyly of Mniaceae and supported the transfer of the Pohlia genus into Mniaceae.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"6"},"PeriodicalIF":1.3,"publicationDate":"2024-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142774935","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":"Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica.","authors":"Mengxin Yu, Mingzhu Bai, Mengmeng Chen, Guozhe Zhang, Yu Zhao, Qingqing Ma, Liyuan Yang, Cuihua Gu","doi":"10.1007/s10709-024-00215-2","DOIUrl":"10.1007/s10709-024-00215-2","url":null,"abstract":"<p><p>The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"179-197"},"PeriodicalIF":1.3,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142373609","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}