IF 1.3 4区生物学

Genetica Pub Date : 2025-06-10 DOI: 10.1007/s10709-025-00236-5

Li-Ming Hang, Zhi-Ping Zhang, Xiao-Hui Zhang, Ya-Kun Li, Qin-Qin Li

{"title":"Comparative chloroplast genome analyses of potentilleae: insights into genome characteristics, mutational hotspots, and adaptive evolution.","authors":"Li-Ming Hang, Zhi-Ping Zhang, Xiao-Hui Zhang, Ya-Kun Li, Qin-Qin Li","doi":"10.1007/s10709-025-00236-5","DOIUrl":"https://doi.org/10.1007/s10709-025-00236-5","url":null,"abstract":"Potentilleae Sweet is a large tribe within Rosaceae Juss., with over 1700 species across 13 genera worldwide. Some achievements have been obtained in the study of phylogenetic relationships among Potentilleae genera and its origin and diversification, while its chloroplast (cp.) genome characteristics, mutational hotspots and adaptive evolution are still open questions. In this study, we conducted comparative genomic study on 79 complete cp. genomes of Potentilleae. The Potentilleae cp. genome has a typical quadripartite structure, with a total length of 150,586 - 156,798 bp and Guanine and cytosine (GC) content of 36.7-37.3%. Although some slight differences were present in cp. genome size, GC content, and inverted repeat (IR)/single-copy (SC) boundary regions, gene structure, gene content and gene order of the Potentilleae cp. genome were conserved. Thirteen regions (psaJ-rpl33, rpl16-rps3, petA-psbJ, rpl16 intron, rpl32-trnL-UAG, trnH-GUG-psbA, trnR-UCU-atpA, ndhG-ndhI, accD-psaI, trnL-UAA-trnF-GAA, trnP-UGG-psaJ, ycf4-cemA, ndhC-trnV-UAC) were identified as excellent molecular markers for phylogenetic application. Twenty-three genes (rps16, rpl20, rpl22, rpl23, rpoA, rpoC2, psaA, psbB, psbC, psbH, psbF, psbJ, rbcL, ndhA, ndhB, ndhD, ndhF, ndhI, accD, ccsA, matK, ycf1, ycf2) were positively selected. The adaptive evolution of these genes might play essential roles in the long evolutionary history of Potentilleae. This study will lay a foundation for the future research on identification, phylogeny and adaptive evolution of Potentilleae species.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"22"},"PeriodicalIF":1.3,"publicationDate":"2025-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144259422","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}

引用次数: 0

Genome-wide identification of bHLH transcription factors related to plant development and abiotic stress response in sand rice (Agriophyllum squarrosum (L.) Moq.)). 沙稻（Agriophyllum squarrosum， L.）植株发育及非生物胁迫应答相关bHLH转录因子的全基因组鉴定Moq。))。

IF 1.3 4区生物学

Genetica Pub Date : 2025-06-04 DOI: 10.1007/s10709-025-00238-3

Ruizhen Zhang, Xiaoyun Cui, Xiaofeng Li, Pengshan Zhao

{"title":"Genome-wide identification of bHLH transcription factors related to plant development and abiotic stress response in sand rice (Agriophyllum squarrosum (L.) Moq.)).","authors":"Ruizhen Zhang, Xiaoyun Cui, Xiaofeng Li, Pengshan Zhao","doi":"10.1007/s10709-025-00238-3","DOIUrl":"https://doi.org/10.1007/s10709-025-00238-3","url":null,"abstract":"Sand rice (Agriophyllum squarrosum (L.) Moq.) is widely distributed across mobile and semi-mobile sand dunes in Central Asia and can thrive in extreme environments, including drought, salinity, high temperatures, and UV radiation. The basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in plant growth and development, as well as in responses to various environmental stresses. However, a comprehensive analysis of the bHLH family in sand rice has not yet been conducted. In this study, a total of 69 bHLH genes (AsbHLHs) were identified and classified into 18 subfamilies based on phylogenetic analysis. Their physicochemical properties, bHLH domains, conserved motifs, and gene structures were further examined. Most AsbHLHs within the same subfamily shared similar characteristics. cis-Regulatory elements (CREs) and Gene Ontology (GO) analyses suggested that AsbHLHs are involved in plant development, hormonal signaling, and stress responses. Transcriptomic analysis revealed tissue- and stress-responsive-specific expression profiles of AsbHLHs. qRT-PCR validation confirmed the expression of 69 AsbHLHs across different tissues and 17 genes under salt and drought stress, with AsbHLH7, 10, 20, 22, 32, 46, 53, 59, 64, 65, 68, and 69 proposed as potential regulators in stress response. Protein-protein interaction network predications showed that these proteins may potentially form complexes, which could participate in stress-related biological processes. Statistical analyses, including Mantel's test and redundancy analysis (RDA), revealed significant correlations between gene structural features and expression profiles. These findings suggest a potential framework for exploring the role of bHLH TFs in stress tolerance and adaptive mechanisms in sand rice.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"21"},"PeriodicalIF":1.3,"publicationDate":"2025-06-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144217630","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}

引用次数: 0

Characterization of five complete mitochondrial genomes of the genus Simulium (Diptera: Simuliidae) and their phylogenetic implications. 拟蝇属（双翅目：拟蝇科）5个线粒体全基因组的特征及其系统发育意义。

IF 1.3 4区生物学

Genetica Pub Date : 2025-05-17 DOI: 10.1007/s10709-025-00237-4

Yanxia He, Shifei Xiang, Hongbin Luo, Dali Chen, Xianguang Guo

{"title":"Characterization of five complete mitochondrial genomes of the genus Simulium (Diptera: Simuliidae) and their phylogenetic implications.","authors":"Yanxia He, Shifei Xiang, Hongbin Luo, Dali Chen, Xianguang Guo","doi":"10.1007/s10709-025-00237-4","DOIUrl":"https://doi.org/10.1007/s10709-025-00237-4","url":null,"abstract":"Black flies (family Simuliidae) are globally distributed insects of great medical and veterinary importance. However, little is known about their mitogenomics. Therefore, in this study, the mitochondrial genomes (mitogenomes) of five black fly species‒Simulium bidentatum, S. siripoomense, S. fenestratum, S. chamlongi, S. quinquestriatum‒were sequenced using next-generation sequencing. We conducted a comprehensive comparative analysis of these mitogenomes focusing on sequence length, A + T content, A/T bias, A + T- rich regions, overlapping and intergenic regions, nucleotide composition, relative synonymous codon usage, and the non-synonymous/synonymous substitution ratio (Ka/Ks). Additionally, we analyzed the phylogenetic implications in combination with the Simuliidae and Nematocera species available in GenBank. The mitogenomes ranged from 15,739 to 16,451 base pairs (bp); each contained 37 genes, with no gene rearrangements. The tRNASer (Ser1) lacks the dihydrouridine arm. Selection pressure analysis of 13 PCGs in 45 Nematocera mitogenomes revealed that nd2, nd5, nd4 l, and nd1 had Ka/Ks ratios greater than 1, indicating higher rates of non-synonymous substitutions. In contrast, cox1 showed the lowest Ka/Ks values, indicating strong purifying selection. Phylogenetic analyses supported the monophyly of each subgenus within Simulium, but revealed different subgeneric relationships compared to previous studies. We also observed that different samples can yield different phylogenetic results for higher level relationships within Culicomorpha. The phylogenetic position of Anisopodidae within the Bibionomorpha remains unclear and warrants further investigation.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"20"},"PeriodicalIF":1.3,"publicationDate":"2025-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144087076","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}

引用次数: 0

Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae. 黄花蔷薇（picelellobium dulce）叶绿体基因组比较分析底1844号及其科内的近缘种。

IF 1.3 4区生物学

Genetica Pub Date : 2025-05-06 DOI: 10.1007/s10709-025-00234-7

Hoang Danh Nguyen, Ngoc Han Vu, Hoang Dang Khoa Do, Minh Thiet Vu

{"title":"Comparative chloroplast genomic analysis of Pithecellobium dulce (Roxb.) Benth 1844 and related species within Caesalpinioideae.","authors":"Hoang Danh Nguyen, Ngoc Han Vu, Hoang Dang Khoa Do, Minh Thiet Vu","doi":"10.1007/s10709-025-00234-7","DOIUrl":"https://doi.org/10.1007/s10709-025-00234-7","url":null,"abstract":"The genus Pithecellobium Mart. (Caesalpinioideae, Fabaceae) plays vital ecological roles, including nitrogen fixation and habitat stabilization, and holds significant medicinal and economic values. However, its genetic diversity and evolutionary relationships remain poorly understood. This study presents the first complete chloroplast (cp.) genome of Pithecellobium dulce (Roxb.) Benth., a widely distributed tropical tree. The complete cp. genome was assembled de novo using NOVOPlasty and annotated with GeSeq and Geneious Prime. Repeat elements and codon usage analyses were analyzed using REPuter, Phobos, and Geneious Prime. Comparative genomic analyses included structural comparisons, IR expansion/contraction, and nucleotide divergence. Phylogenetic relationships were inferred from protein-coding genes using IQ-TREE and MrBayes, with divergence times estimated via BEAST2. The cp. genome of P. dulce was 179,483 bp long, exhibiting a typical quadripartite structure with a large single-copy (LSC) region of 91,513 bp, a small single-copy (SSC) region of 4,560 bp, and two inverted repeat regions (IRs) of 41,705 bp each. It encoded 142 genes, including 97 protein-coding genes, 37 tRNA genes, and eight rRNA genes. Comparative analysis revealed a conserved genomic structure within the Pithecellobium subclade, with notable IR expansion into SSC and LSC regions. Phylogenetic analysis placed P. dulce within the Pithecellobium subclade, closely related to Ebenopsis ebano Britton & Rose and Havardia acatlensis (Benth.) Britton & Rose. Divergence time estimates suggest that Pithecellobium subclade diverged in the late Miocene (~ 29.96 Ma), with P. dulce and E. ebano separating around 16.79 Ma. This study provides an essential genomic resource for resolving phylogenetic relationships and advancing taxonomic research in Caesalpinioideae.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"19"},"PeriodicalIF":1.3,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144057448","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}

引用次数: 0

Identification, characterization, and evolutionary analysis of aldehyde dehydrogenase (ALDH) genes superfamily in Medicago truncatula L. 苜蓿醛脱氢酶（ALDH）基因超家族的鉴定、特征及进化分析。

IF 1.3 4区生物学

Genetica Pub Date : 2025-05-03 DOI: 10.1007/s10709-025-00235-6

Somayeh Allahi, Amin Abedi, Hassan Hassani Kumleh, M Mehdi Sohani

{"title":"Identification, characterization, and evolutionary analysis of aldehyde dehydrogenase (ALDH) genes superfamily in Medicago truncatula L.","authors":"Somayeh Allahi, Amin Abedi, Hassan Hassani Kumleh, M Mehdi Sohani","doi":"10.1007/s10709-025-00235-6","DOIUrl":"https://doi.org/10.1007/s10709-025-00235-6","url":null,"abstract":"Aldehydes are reactive compounds that play crucial roles in various metabolic processes within plants. However, their accumulation can lead to toxic effects, Aldehyde dehydrogenases (ALDHs) represent a diverse family of enzymes that catalyze the oxidation of aldehydes to carboxylic acids. ALDHs help mitigate the toxic effects of these compounds and maintain cellular homeostasis in plants. In this study, a bioinformatics analysis of the Medicago truncatula genome identified 27 MtALDHs, which were classified into ten distinct groups based on their phylogenetic relationships. The distribution of these families across the chromosomes of M. truncatula is uneven, with segmental duplications being the primary factor contributing to the expansion of this gene family within the species. The gene structure and motif analysis within each ALDH family in M. truncatula, along with its orthologous genes in Arabidopsis, exhibits a high degree of conservation. The promoter region analysis of these genes reveals a rich abundance of cis-regulatory elements that respond to various environmental stresses and hormones. Furthermore, examination of the expression patterns of MtALDH genes using available microarray data indicated that several of these genes exhibit high expression levels throughout all developmental stages in M. truncatula. Additionally, some genes display tissue-specific expression and are induced in response to salt stress, suggesting a significant role for these genes in growth processes and stress responses within M. truncatula. The findings from this study provide essential insights and data necessary for the functional evaluation of each MtALDH gene during developmental stages and in response to environmental stresses.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"18"},"PeriodicalIF":1.3,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144040961","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}

引用次数: 0

Genome-wide identification and expression analysis of PP2C gene families in two Chimonanthus species. 两种chimonthus属植物PP2C基因家族的全基因组鉴定及表达分析。

IF 1.3 4区生物学

Genetica Pub Date : 2025-05-03 DOI: 10.1007/s10709-025-00233-8

Xin-Chen He, Jie-Xin Shao, Wei Zou, Shu-Xiao Zhang, Li Zhu, Meng-Cheng Ji, Cui-Hua Gu, Li-Yuan Yang

{"title":"Genome-wide identification and expression analysis of PP2C gene families in two Chimonanthus species.","authors":"Xin-Chen He, Jie-Xin Shao, Wei Zou, Shu-Xiao Zhang, Li Zhu, Meng-Cheng Ji, Cui-Hua Gu, Li-Yuan Yang","doi":"10.1007/s10709-025-00233-8","DOIUrl":"https://doi.org/10.1007/s10709-025-00233-8","url":null,"abstract":"The protein phosphatase 2 C (PP2C) plays a crucial role in the growth and development of plants. However, limited information on the PP2C genes in Chimonanthus spp. is available. Therefore, the comprehensive genome-wide identification and analysis of the PP2Cs gene family is necessary in Chimonanthus spp. to provide basic information for further study. In this work, 93 members of the CsPP2C gene family and 85 members of the CpPP2C gene family were identified. Based on the phylogenetic analysis, 93 CsPP2Cs and 85 CpPP2Cs genes were classified into 13 subgroups. Based on RNA-Seq data, specific expression patterns of CsPP2Cs in different tissues were identified. CsPP2C28, CsPP2C55, and CsPP2C17 showed high expression during leaf senescence, and combined with cis-element analysis, it is speculated that they may participate in regulating plant senescence. CsPP2C47, CsPP2C27, CsPP2C42, and CsPP2C41 may play an important role in responding to abscisic acid during seed dormancy and germination. These results contribute to a deeper understanding of the functions of the CsPP2C gene family and CpPP2C gene family, and providing candidate genes for genetic engineering and breeding to enhance important traits such as stress resistance and growth development in C. salicifolius and C. praecox.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"17"},"PeriodicalIF":1.3,"publicationDate":"2025-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144035953","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}

引用次数: 0

Temporal and habitat adaptations in Drosophila subobscura populations: changes in chromosomal inversions. 亚bobscura果蝇种群的时间和栖息地适应：染色体倒位的变化。

IF 1.3 4区生物学

Genetica Pub Date : 2025-04-25 DOI: 10.1007/s10709-025-00232-9

Goran Zivanovic, Concepció Arenas, Francesc Mestres

{"title":"Temporal and habitat adaptations in Drosophila subobscura populations: changes in chromosomal inversions.","authors":"Goran Zivanovic, Concepció Arenas, Francesc Mestres","doi":"10.1007/s10709-025-00232-9","DOIUrl":"https://doi.org/10.1007/s10709-025-00232-9","url":null,"abstract":"In insects, chromosomal inversion polymorphism has been related with different adaptations, including global warming. Regarding this environmental change, Drosophila subobscura stands out as a useful model species due to its rich inversion polymorphism covering the whole karyotype. The main aims of this research were to analyze the differentiation of this polymorphism in Jastrebac Mt. (Serbia) depending on the different habitats (beech and oak forests) and over time. These latter changes were studied in relation to climatic variables (mean, minimum and maximum temperatures, humidity and rainfall). Microdifferentiation was observed between beech and oak forests, mainly for the A and O chromosomes. However, the changes over time turned out to be larger than those due to habitat. In Jastrebac Mt., temperatures increased over time, with this increase being significant for mean and minimum one. The Multidimensional Scaling analysis showed a relation between chromosomal inversions and temperatures (mainly minimum) in Jastrebac Mt. and other Serbian populations of D. subobscura. In beech forest of Jastrebac Mt., the Chromosomal Thermal Index increased over time from 1990 to 1994, but showing a possible stabilization in 2023. This result was observed in other studied Serbian populations. Although those are preliminary results, it might hypothesize that there may be a threshold for the action of natural selection, increasing 'warm' adaptive inversions and decreasing 'cold' ones. The possible reasons for this hypothesis are also discussed.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"16"},"PeriodicalIF":1.3,"publicationDate":"2025-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12031780/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144053167","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}

引用次数: 0

Phylomitogenomics supports Actias Isabellae (Graells, 1849) as the definitive scientific name of the Spanish Moon Moth (Lepidoptera, Saturniidae). 植物基因组学支持Actias Isabellae （Graells, 1849）作为西班牙月蛾（鳞翅目，土星科）的最终学名。

IF 1.3 4区生物学

Genetica Pub Date : 2025-03-24 DOI: 10.1007/s10709-025-00231-w

Daniel García-Souto, Sonia Zumalave, Juan M Martínez-Romero, Neus Marí-Mena, Antón Vizcaíno, Marta Vila

{"title":"Phylomitogenomics supports Actias Isabellae (Graells, 1849) as the definitive scientific name of the Spanish Moon Moth (Lepidoptera, Saturniidae).","authors":"Daniel García-Souto, Sonia Zumalave, Juan M Martínez-Romero, Neus Marí-Mena, Antón Vizcaíno, Marta Vila","doi":"10.1007/s10709-025-00231-w","DOIUrl":"10.1007/s10709-025-00231-w","url":null,"abstract":"The taxonomic classification of the Spanish Moon Moth has been contentious for over a century, with debates over its placement within the genera Graellsia and Actias. This study presents a comprehensive analysis of the complete mitochondrial genome (mitogenome) of this iconic insect, revealing a closed circular molecule of 15,252 bp containing 37 genes, consistent with the mitochondrial genomes of other Lepidoptera. Phylomitogenomic analyses confirm that the Spanish Moon Moth clusters monophyletically with Actias dubernardi and the other species of this genus, supporting the assertion that Graellsia is a junior synonym of Actias. Our findings further highlight that the shared ancestry of these species suggests a common evolutionary origin for the pine-feeding trait, challenging previous notions of parallel evolution. The implications of this taxonomic revision are significant, as Actias isabellae is protected under various European conservation laws. This research provides the crucial genetic data necessary for the formal recognition of Actias isabellae, potentially prompting updates to legal classifications and enhancing our understanding of Lepidopteran biodiversity.","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"15"},"PeriodicalIF":1.3,"publicationDate":"2025-03-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11933237/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143702384","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}

引用次数: 0

Differential DNA methylation in response to host environment changes in Drosophila gouveai. 果蝇对宿主环境变化的差异DNA甲基化反应。

IF 1.3 4区生物学

Genetica Pub Date : 2025-03-08 DOI: 10.1007/s10709-025-00230-x

Adriano S Santos, Ester S Ramos, Vera L S Valente, Maura H Manfrin

{"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":"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.","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}

引用次数: 0

New insights into the adaptation mechanism of Cardisoma armatum hepatopancreas in the terrestrial environment by transcriptome analysis. 通过转录组分析，对陆地环境下野心肝胰腺的适应机制有了新的认识。

IF 1.3 4区生物学

Genetica Pub Date : 2025-03-06 DOI: 10.1007/s10709-025-00229-4

Zhengfei Wang, Sijia Hao, Chenchen Shen, Jinghao Hu, Yayun Guan, Zhuofan Chen, Shang Zhu, Xinyu Wang, Lv Wu

{"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":"10.1007/s10709-025-00229-4","url":null,"abstract":"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.","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}

引用次数: 0

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