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Microsatellite based molecular characterization of Nattukuttai- a unique short statured Bos indicus cattle population of southern India. 基于微卫星的 Nattukuttai 分子特征研究--印度南部一个独特的短身材波士牛种群。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-11-15 DOI: 10.1007/s10709-024-00219-y
Ymberzal Koul, S M K Karthickeyan, P Hepsibha, C Jeevan, K Thilak Pon Jawahar, A Gopinathan
{"title":"Microsatellite based molecular characterization of Nattukuttai- a unique short statured Bos indicus cattle population of southern India.","authors":"Ymberzal Koul, S M K Karthickeyan, P Hepsibha, C Jeevan, K Thilak Pon Jawahar, A Gopinathan","doi":"10.1007/s10709-024-00219-y","DOIUrl":"10.1007/s10709-024-00219-y","url":null,"abstract":"<p><p>Molecular characterization was conducted to characterise 'Nattukuttai', a native cattle population of the north-eastern agro-climatic zone of Tamil Nadu (India), using thirty microsatellite markers. The analyses revealed a high level of genetic diversity, with a total of 294 alleles observed across all the loci, averaging 9.8 alleles per locus. The allele sizes ranged from 83 bp to 302 bp, with frequencies ranging from 0.010 to 0.875. The microsatellite markers demonstrated high polymorphism, as indicated by an average polymorphic information content (PIC) of 0.763. Deviation from Hardy-Weinberg equilibrium was observed in a significant number of loci, indicating possible genetic influences such as selection or population structure. Bottleneck analysis suggested that the Nattukuttai population did not undergo any recent significant population contraction. Comparative analyses with three other cattle populations (Kangayam, Malai Madu, and Malnad Gidda) revealed varying genetic distances. Nattukuttai showed a distinct genetic profile, diverging from a common source that also gave rise to the Kangayam and Malai Madu clusters. Multivariate statistical analyses and phylogenetic reconstruction supported the genetic differentiation of Nattukuttai from the other populations, while Malai Madu and Kangayam were found to be genetically closer to each other. Overall, these findings provide insights into the genetic structure and relationships of the Nattukuttai cattle population, highlighting its distinct genetic identity and potential conservation significance.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"153 1","pages":"1"},"PeriodicalIF":1.3,"publicationDate":"2024-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142640348","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 and expression analysis of XIP gene family members in rice. 水稻中 XIP 基因家族成员的鉴定和表达分析
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-14 DOI: 10.1007/s10709-024-00207-2
Manman Zhao, Zhiwei Liu, Jiangtao Gan, Chen Yang, Ai Lu, Qingqing Han, Haitao Yang, Yonghan Xu, Genlou Sun, Dechuan Wu
{"title":"Identification and expression analysis of XIP gene family members in rice.","authors":"Manman Zhao, Zhiwei Liu, Jiangtao Gan, Chen Yang, Ai Lu, Qingqing Han, Haitao Yang, Yonghan Xu, Genlou Sun, Dechuan Wu","doi":"10.1007/s10709-024-00207-2","DOIUrl":"10.1007/s10709-024-00207-2","url":null,"abstract":"<p><p>Xylanase inhibitor proteins (XIP) are widely distributed in the plant kingdom, and also exist in rice. However, a systematic bioinformatics analysis of this gene family in rice (OsXIP) has not been conducted to date. In this study, we identified 32 members of the OsXIP gene family and analyzed their physicochemical properties, chromosomal localization, gene structure, protein structure, expression profiles, and interaction networks. Our results indicated that OsXIP genes exhibit an uneven distribution across eight rice chromosomes. These genes generally feature a low number of introns or are intronless, all family members, except for OsXIP20, contain two highly conserved motifs, namely Motif 8 and Motif 9. In addition, it is worth noting that the promoter regions of OsXIP gene family members feature a widespread presence of abscisic acid response elements (ABRE) and gibberellin response elements (GARE-motif and TATC-box). Quantitative Real-time PCR (qRT-PCR) analysis unveiled that the expression of OsXIP genes exhibited higher levels in leaves and roots, with considerable variation in the expression of each gene in these tissues both prior to and following treatments with abscisic acid (ABA) and gibberellin (GA3). Protein interaction studies and microRNA (miRNA) target prediction showed that OsXIP engages with key elements within the hormone-responsive and drought signaling pathways. The qRT-PCR suggested osa-miR2927 as a potential key regulator in the rice responding to drought stress, functioning as tissue-specific and temporally regulation. This study provides a theoretical foundation for further analysis of the functions within the OsXIP gene family.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"83-100"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140923811","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 the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa. 拟南芥、玉米和大豆中通用应激蛋白(USP)基因家族的全基因组鉴定和表达分析。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-24 DOI: 10.1007/s10709-024-00209-0
Mingxia Fan, Song Gao, Yating Yang, Shuang Yang, He Wang, Lei Shi
{"title":"Genome-wide identification and expression analysis of the universal stress protein (USP) gene family in Arabidopsis thaliana, Zea mays, and Oryza sativa.","authors":"Mingxia Fan, Song Gao, Yating Yang, Shuang Yang, He Wang, Lei Shi","doi":"10.1007/s10709-024-00209-0","DOIUrl":"10.1007/s10709-024-00209-0","url":null,"abstract":"<p><p>The Universal Stress Protein (USP) primarily participates in cellular responses to biotic and abiotic stressors, playing a pivotal role in plant growth, development, and Stress responses to adverse environmental conditions. Totals of 23, 26 and 26 USP genes were recognized in Arabidopsis thaliana, Zea mays, and Oryza sativa, respectively. According to USP genes physicochemical properties, proteins from USP I class were identified as hydrophilic proteins with high stability. Based on phylogenetic analysis, USP genes family were classified into nine groups, USP II were rich in motifs. Additionally, members of the same subgroup exhibited similar numbers of introns/exons, and shared conserved domains, indicating close evolutionary relationships. Motif analysis results demonstrated a high degree of conservation among USP genes. Chromosomal distribution suggested that USP genes might have undergone gene expansion through segmental duplication in Arabidopsis thaliana, Zea mays, and Oryza sativa. Most Ka/Ks ratios were found to be less than 1, suggesting that USP genes in Arabidopsis thaliana, Zea mays, and Oryza sativa have experienced purifying selection. Expression profile analysis revealed that USP genes primarily respond to drought stress in Oryza sativa, temperature, and drought stress in Zea mays, and cold stress in Arabidopsis thaliana. Gene collinearity analysis can reveal correlations between genes, aiding subsequent in-depth investigations. This study sheds new light on the evolution of USP genes in monocots and dicots and lays the foundation for a better understanding of the biological functions of the USP genes family.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"119-132"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141094672","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
A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus. 脆弱淡水鲑鱼(Thymallus ligericus)的多组织从头转录组组装和相对基因表达。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-06-18 DOI: 10.1007/s10709-024-00210-7
Giulia Secci-Petretto, Steven Weiss, André Gomes-Dos-Santos, Henri Persat, André M Machado, Inês Vasconcelos, L Filipe C Castro, Elsa Froufe
{"title":"A multi-tissue de novo transcriptome assembly and relative gene expression of the vulnerable freshwater salmonid Thymallus ligericus.","authors":"Giulia Secci-Petretto, Steven Weiss, André Gomes-Dos-Santos, Henri Persat, André M Machado, Inês Vasconcelos, L Filipe C Castro, Elsa Froufe","doi":"10.1007/s10709-024-00210-7","DOIUrl":"10.1007/s10709-024-00210-7","url":null,"abstract":"<p><p>Freshwater ecosystems are among the most endangered ecosystems worldwide. While numerous taxa are on the verge of extinction as a result of global changes and direct or indirect anthropogenic activity, genomic and transcriptomic resources represent a key tool for comprehending species' adaptability and serve as the foundation for conservation initiatives. The Loire grayling, Thymallus ligericus, is a freshwater European salmonid endemic to the upper Loire River basin. The species is comprised of fragmented populations that are dispersed over a small area and it has been identified as a vulnerable species. Here, we provide a multi-tissue de novo transcriptome assembly of T. ligericus. The completeness and integrity of the transcriptome were assessed before and after redundancy removal with lineage-specific libraries from Eukaryota, Metazoa, Vertebrata, and Actinopterygii. Relative gene expression was assessed for each of the analyzed tissues, using the de novo assembled transcriptome and a genome-based analysis using the available T. thymallus genome as a reference. The final assembly, with a contig N50 of 1221 and Benchmarking Universal Single-Copy Orthologs (BUSCO) scores above 94%, is made accessible along with structural and functional annotations and relative gene expression of the five tissues (NCBI SRA and FigShare databases). This is the first transcriptomic resource for this species, which provides a foundation for future research on this and other salmonid species that are increasingly exposed to environmental stressors.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"71-81"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11199216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141421935","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
Comparative genomic analysis reveals expansion of the DnaJ gene family in Lagerstroemia indica and its members response to salt stress. 比较基因组分析揭示了 Lagerstroemia indica 中 DnaJ 基因家族的扩展及其成员对盐胁迫的响应。
IF 1.3 4区 生物学
Genetica Pub Date : 2024-06-01 Epub Date: 2024-05-10 DOI: 10.1007/s10709-024-00208-1
Jin Qin, Xiaoyu Hou, Huanzhe Wang, Tianyi Yuan, Hui Wei, Guoyuan Liu, Yanhong Chen, Bolin Lian, Fei Zhong, Jian Zhang, Chunmei Yu
{"title":"Comparative genomic analysis reveals expansion of the DnaJ gene family in Lagerstroemia indica and its members response to salt stress.","authors":"Jin Qin, Xiaoyu Hou, Huanzhe Wang, Tianyi Yuan, Hui Wei, Guoyuan Liu, Yanhong Chen, Bolin Lian, Fei Zhong, Jian Zhang, Chunmei Yu","doi":"10.1007/s10709-024-00208-1","DOIUrl":"10.1007/s10709-024-00208-1","url":null,"abstract":"<p><p>DnaJs/Hsp40s/JPDs are obligate co-chaperones of heat shock proteins (Hsp70), performing crucial biological functions within organisms. A comparative genome analysis of four genomes (Vitis vinifera, Eucalyptus grandis, Lagerstroemia indica, and Punica granatum) revealed that the DnaJ gene family in L. indica has undergone expansion, although not to the extent observed in P. granatum. Inter-genome collinearity analysis of four plants indicates that members belonging to Class A and B are more conserved during evolution. In L. indica, the expanded members primarily belong to Class-C. Tissue expression patterns and the biochemical characterization of LiDnaJs further suggested that DnaJs may be involved in numerous biological processes in L. indica. Transcriptome and qPCR analyses of salt stressed leaves identified at least ten LiDnaJs that responded to salt stress. In summary, we have elucidated the expansion mechanism of the LiDnaJs, which is attributed to a recent whole-genome triplication. This research laid the foundation for functional analysis of LiDnaJs and provides gene resources for breeding salt-tolerant varieties of L. indica.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"101-117"},"PeriodicalIF":1.3,"publicationDate":"2024-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140900425","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
Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae) Megaleporinus obtusidens和M. reinhardti(蛛形纲:Anostomidae)的重复DNA和染色体进化
IF 1.5 4区 生物学
Genetica Pub Date : 2024-04-08 DOI: 10.1007/s10709-024-00206-3
Thais Aparecida Dulz, Matheus Azambuja, Carla Andrea Lorscheider, Rafael Bueno Noleto, Orlando Moreira-Filho, Viviane Nogaroto, Viviane Demetrio Nascimento, Débora Diniz, Paulo Roberto Antunes de Mello Affonso, Marcelo Ricardo Vicari
{"title":"Repetitive DNAs and chromosome evolution in Megaleporinus obtusidens and M. reinhardti (Characiformes: Anostomidae)","authors":"Thais Aparecida Dulz, Matheus Azambuja, Carla Andrea Lorscheider, Rafael Bueno Noleto, Orlando Moreira-Filho, Viviane Nogaroto, Viviane Demetrio Nascimento, Débora Diniz, Paulo Roberto Antunes de Mello Affonso, Marcelo Ricardo Vicari","doi":"10.1007/s10709-024-00206-3","DOIUrl":"https://doi.org/10.1007/s10709-024-00206-3","url":null,"abstract":"<p>The high dynamism of repetitive DNAs is a major driver of chromosome evolution. In particular, the accumulation of repetitive DNA sequences has been reported as part of the differentiation of sex-specific chromosomes. In turn, the fish species of the genus <i>Megaleporinus</i> are a monophyletic clade in which the presence of differentiated ZZ/ZW sex chromosomes represents a synapomorphic condition, thus serving as a suitable model to evaluate the dynamic evolution of repetitive DNA classes. Therefore, transposable elements (TEs) and in tandem repeats were isolated and located on chromosomes of <i>Megaleporinus obtusidens</i> and <i>M. reinhardti</i> to infer their role in chromosome differentiation with emphasis on sex chromosome systems. Despite the conserved karyotype features of both species, the location of repetitive sequences - <i>Rex 1</i>, <i>Rex 3</i>, (TTAGGG)<sub>n</sub>, (GATA)<sub>n</sub>, (GA)n, (CA)<sub>n</sub>, and (A)<sub>n</sub> - varied both intra and interspecifically, being mainly accumulated in Z and W chromosomes. The physical mapping of repetitive sequences confirmed the remarkable dynamics of repetitive DNA classes on sex chromosomes that might have promoted chromosome diversification and reproductive isolation in <i>Megaleporinus</i> species.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"12 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2024-04-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140583895","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
Nuclear gene introgressions in hybrid populations of water frog Pelophylax esculentus complex: geographical analysis of the phenomenon and its interpretation. 水蛙(Pelophylax esculentus complex)杂交种群中的核基因导入:现象的地理分析及其解释。
IF 1.5 4区 生物学
Genetica Pub Date : 2024-02-01 Epub Date: 2024-02-15 DOI: 10.1007/s10709-024-00203-6
Sergey V Mezhzherin, Svyatoslav Yu Morozov-Leonov, Olga V Rostovska
{"title":"Nuclear gene introgressions in hybrid populations of water frog Pelophylax esculentus complex: geographical analysis of the phenomenon and its interpretation.","authors":"Sergey V Mezhzherin, Svyatoslav Yu Morozov-Leonov, Olga V Rostovska","doi":"10.1007/s10709-024-00203-6","DOIUrl":"10.1007/s10709-024-00203-6","url":null,"abstract":"<p><p>Reproduction of water frog hybrids Pelophylax esculentus (Pelophylax ridibundus x Pelophylax lessonae) is associated with hemiclonal reproduction and backcrossing. The hemiclonal mode of reproduction occurs within P. esculentus allodiploids. In this case, the unrecombined genome of one parental species is transmitted to the offspring after premeiotic elimination of the chromosome set of the second parental species. Usually, the chromosome set of P. lessonae is eliminated, and the altered genome of P. ridibundus is passed on to the progeny. The hemiclonal inheritance within diploid Pelophylax esculentus hybrids may be accompanied by certain aberrations of premeiotic elimination. As a result, the formation of P. ridibundus specimens with introgressions of the P. lessonae genetic material, or the formation of recombinant hybrids occurs, depending on which of the parental species backcrossing takes place. The aim of our study is to describe the aberration of premeiotic elimination within the water frog P. esculentus complex detected by the nuclear gene Ldh-B inheritance, with an attempt to find out the causes of this phenomenon. It has been established that aberrations of premeiotic elimination are widespread, but only within populations of water frog from the river system of Upper Dnieper within Ukraine. The highest level of introgression takes place in the water frog populations within Kiev metropolis under conditions of expressed anthropogenization, while the maximum frequency of recombinants was detected within populations from the basin of Desna River, that has preserved native ecosystems. It was demonstrated that the frequency of premeiotic aberrations does not correlate with the intensity of interspecific water frog hybridization. Populations with introgressions are more common than populations with recombinants, however, within the latter, the frequency of recombination events is higher. The primary factor of gametogenesis aberrations, most likely, is the genetic characteristics of the local populations of parental species, since unambiguous explanations of this phenomenon based on the action of environmental stress (pollution of water systems) are not obvious.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"31-42"},"PeriodicalIF":1.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139742757","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
Cytomolecular trends in Chamaecrista Moench (Caesalpinioideae, Leguminosae) diversification. Chamaecrista Moench(Caesalpinioideae,豆科)多样化的细胞分子趋势。
IF 1.5 4区 生物学
Genetica Pub Date : 2024-02-01 Epub Date: 2024-02-21 DOI: 10.1007/s10709-024-00205-4
Guilherme Tomaz Braz, Brena Van-Lume, Kátia Ferreira Marques de Resende, Felipe Pereira Cardoso, Ludmila Oliveira, Maria José Gomes de Andrade, Gustavo Souza, Giovana Augusta Torres
{"title":"Cytomolecular trends in Chamaecrista Moench (Caesalpinioideae, Leguminosae) diversification.","authors":"Guilherme Tomaz Braz, Brena Van-Lume, Kátia Ferreira Marques de Resende, Felipe Pereira Cardoso, Ludmila Oliveira, Maria José Gomes de Andrade, Gustavo Souza, Giovana Augusta Torres","doi":"10.1007/s10709-024-00205-4","DOIUrl":"10.1007/s10709-024-00205-4","url":null,"abstract":"<p><p>Chamaecrista is a Pantropical legume genus of the tribe Cassieae, which includes six other genera. In contrast to most of the other Cassieae genera, Chamaecrista shows significant variability in chromosome number (from 2n = 14 to 2n = 56), with small and morphologically similar chromosomes. Here, we performed a new cytomolecular analysis on chromosome number, genome size, and rDNA site distribution in a molecular phylogenetic perspective to interpret the karyotype trends of Chamaecrista and other two genera of Cassieae, seeking to understand their systematics and evolution. Our phylogenetic analysis revealed that Chamaecrista is monophyletic and can be divided into four major clades corresponding to the four sections of the genus. Chromosome numbers ranged from 2n = 14, 16 (section Chamaecrista) to 2n = 28 (sections Absus, Apoucouita, and Baseophyllum). The number of 5S and 35S rDNA sites varied between one and three pairs per karyotype, distributed on different chromosomes or in synteny, with no obvious phylogenetic significance. Our data allowed us to propose x = 7 as the basic chromosome number of Cassieae, which was changed by polyploidy generating x = 14 (sections Absus, Apoucouita, and Baseophyllum) and by ascending dysploidy to x = 8 (section Chamaecrista). The DNA content values supported this hypothesis, with the genomes of the putative tetraploids being larger than those of the putative diploids. We hypothesized that ascending dysploidy, polyploidy, and rDNA amplification/deamplification are the major events in the karyotypic diversification of Chamaecrista. The chromosomal marks characterized here may have cytotaxonomic potential in future studies.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"51-61"},"PeriodicalIF":1.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139914082","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
Differential amplification of the subtelomeric satellite DNA JcSAT1 in the genus Jatropha L. (Euphorbiaceae). 麻风树属(大戟科)亚群卫星 DNA JcSAT1 的差异扩增。
IF 1.5 4区 生物学
Genetica Pub Date : 2024-02-01 Epub Date: 2024-02-13 DOI: 10.1007/s10709-024-00204-5
Tiago Ribeiro, Emanuelle Vasconcelos, José Roseno de Mendonça Filho, Shusei Sato, Daniela de Argollo Marques, Ana Christina Brasileiro-Vidal
{"title":"Differential amplification of the subtelomeric satellite DNA JcSAT1 in the genus Jatropha L. (Euphorbiaceae).","authors":"Tiago Ribeiro, Emanuelle Vasconcelos, José Roseno de Mendonça Filho, Shusei Sato, Daniela de Argollo Marques, Ana Christina Brasileiro-Vidal","doi":"10.1007/s10709-024-00204-5","DOIUrl":"10.1007/s10709-024-00204-5","url":null,"abstract":"<p><p>Satellite DNAs (satDNAs) are highly repetitive sequences that occur in virtually all eukaryotic genomes and can undergo rapid copy number and nucleotide sequence variation among relatives. After chromosomal mapping of the satDNA JcSAT1, it was found a large accumulation at subtelomeres of Jatropha curcas (subgenus Curcas), but an absence of these monomers in J. integerrima (subgenus Jatropha). This fact suggests a dynamic scenario for this satellite repeat in Jatropha genomes. Here, we used a multitasking approach (sequence analysis, DNA blotting and chromosomal mapping) to investigate the molecular organization and chromosomal abundance and distribution of JcSAT1 in a broader group of species from the subgenus Jatropha (J. gossypiifolia, J. mollissima, J. podagrica, and J. multifida) in addition to J. curcas, with the aiming of understanding the evolution of this satDNA. Based on the analysis of BAC clone sequences of J. curcas, a large array (~ 30 kb) of 80 homogeneous monomers of JcSAT1 was identified in BAC 23J11. The monomer size was conserved (~ 358 bp) and contained a telomeric motif at the 5' end. PCR amplification coupled with a Southern blot revealed the presence of JcSAT1-like sequences in all species examined. However, a large set of genome copies was identified only in J. curcas, where a ladder-like pattern with multimers of different sizes was observed. In situ hybridization of BAC 23J11 confirmed the subtelomeric pattern for J. curcas, but showed no signals on chromosomes of species from the subgenus Jatropha. Our data indicate that JcSAT1 is a highly homogeneous satDNA that originated from a region near the telomeres and spread throughout the chromosomal subtermini, possibly due to frequent ectopic recombination between these regions. The abundance of JcSAT1 in the genome of J. curcas suggests that an amplification event occurred either at the base of the subgenus Curcas or at least in this species, although the repeat is shared by all species of the genus studied so far.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"43-49"},"PeriodicalIF":1.5,"publicationDate":"2024-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139725098","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
Genetic basis and repeatability for desiccation resistance in Drosophila melanogaster (Diptera: Drosophilidae) 黑腹果蝇(双翅目:果蝇科)抗干燥性的遗传基础和可重复性
IF 1.5 4区 生物学
Genetica Pub Date : 2023-12-16 DOI: 10.1007/s10709-023-00201-0
{"title":"Genetic basis and repeatability for desiccation resistance in Drosophila melanogaster (Diptera: Drosophilidae)","authors":"","doi":"10.1007/s10709-023-00201-0","DOIUrl":"https://doi.org/10.1007/s10709-023-00201-0","url":null,"abstract":"<h3>Abstract</h3> <p>Dehydration is a stress factor for organisms inhabiting natural habitats where water is scarce. Thus, it may be expected that species facing arid environments will develop mechanisms that maximize resistance to desiccation. Insects are excellent models for studying the effects of dehydration as well as the mechanisms and processes that prevent water loss since the effect of desiccation is greater due to the higher area/volume ratio than larger animals. Even though physiological and behavioral mechanisms to cope with desiccation are being understood, the genetic basis underlying the mechanisms related to variation in desiccation resistance and the context-dependent effect remain unsolved. Here we analyze the genetic bases of desiccation resistance in <em>Drosophila melanogaster</em> and identify candidate genes that underlie trait variation. Our quantitative genetic analysis of desiccation resistance revealed sexual dimorphism and extensive genetic variation. The phenotype-genotype association analyses (GWAS) identified 71 candidate genes responsible for total phenotypic variation in desiccation resistance. Half of these candidate genes were sex-specific suggesting that the genetic architecture underlying this adaptive trait differs between males and females. Moreover, the public availability of desiccation data analyzed on the same lines but in a different lab allows us to investigate the reliability and repeatability of results obtained in independent screens. Our survey indicates a pervasive micro-environment lab-dependent effect since we did not detect overlap in the sets of genes affecting desiccation resistance identified between labs.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"13 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138686438","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}
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