Genetica最新文献

{"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}

{"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}

{"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)_n, (GATA)_n, (GA)n, (CA)_n, and (A)_n - 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}

{"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}

{"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}

{"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}

{"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}

{"title":"Insulin and circadian rhythm genes of the Nile rat (Arvicanthis niloticus) are conserved and orthologous to those in the rat, mouse and human","authors":"Soon-Sen Leow, Jia-Shiun Khoo, Siuk-Mun Ng, Wei-Kang Lee, Chee-Choong Hoh, Syed Fairus, Ravigadevi Sambanthamurthi, K. C. Hayes","doi":"10.1007/s10709-023-00202-z","DOIUrl":"https://doi.org/10.1007/s10709-023-00202-z","url":null,"abstract":"<p>The African grass or Nile rat (NR) (<i>Arvicanthis niloticus</i>) is a herbivorous diurnal rodent which is used as a biological model for research on type 2 diabetes mellitus (T2DM) and the circadian rhythm. Similar to humans, male NRs develop T2DM with high-carbohydrate diets. The NR thus provides a unique opportunity to identify the nutritional and underlying genetic factors that characterise human T2DM, as well as the effects of potential anti-diabetic phytochemicals such as Water-Soluble Palm Fruit Extract. Whole genome sequencing (WGS) could help identify possible genetic causes why NRs spontaneously develop T2DM in captivity. In this study, we performed WGS on a hepatic deoxyribonucleic acid (DNA) sample isolated from a male NR using PacBio high-fidelity long-read sequencing. The WGS data obtained were then <i>de novo</i> assembled and annotated using PacBio HiFi isoform sequencing (Iso-Seq) data as well as previous Illumina RNA sequencing (RNA-Seq) data. Genes related to insulin and circadian rhythm pathways were present in the NR genome, similar to orthologues in the rat, mouse and human genomes. T2DM development in the NR is thus most likely not attributable to structural differences in these genes when compared to other biological models. Further studies are warranted to gain additional insights on the genetic-environmental factors which underlie the <i>genetic permissiveness</i> of NRs to develop T2DM.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"85 1","pages":""},"PeriodicalIF":1.5,"publicationDate":"2023-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138686274","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":"Methods for two nonstandard problems arising from the Luria-Delbrück experiment.","authors":"Qi Zheng","doi":"10.1007/s10709-023-00200-1","DOIUrl":"10.1007/s10709-023-00200-1","url":null,"abstract":"<p><p>The fluctuation experiment, devised by Luria and Delbrück in 1943, remains the method of choice for measuring microbial mutation rates in the laboratory. While most inference problems commonly encountered in a fluctuation experiment can be tackled by existing standard algorithms, investigators from time to time run into nonstandard problems not amenable to any existing algorithms. A major obstacle to solving these nonstandard problems is the construction of confidence intervals for mutation rates. This note describes methods for two important categories of nonstandard problems, namely, pooling data from separate experiments and analyzing grouped mutant count data, focusing on the construction of likelihood ratio confidence intervals. In addition to illustrative examples using real-world data, simulation results are presented to help assess the proposed methods.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"369-373"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138447149","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":"Forecasting effects of climate changes on the population genetic structure of Anacardium occidentale in the Cerrado biome, Brazil.","authors":"Jacqueline Souza Lima, Rosane Garcia Collevatti, Leciane Kárita de Oliveira, Lázaro José Chaves, Ronaldo Veloso Naves, Thannya Nascimento Soares, José Alexandre Felizola Diniz Filho, Mariana Pires de Campos Telles","doi":"10.1007/s10709-023-00199-5","DOIUrl":"10.1007/s10709-023-00199-5","url":null,"abstract":"<p><p>There has been a continuous interest in understanding the patterns of genetic diversity in natural populations because of the role of intraspecific genetic diversity as the basis of all evolutionary change and thus, its potential effects on population persistence when facing environmental changes. Here, we provided the first description of genetic diversity distribution and population structure of Anacardium occidentale L. (cashew) from the Brazilian Cerrado, one of the most economically important tropical crops in the world. We applied Bayesian clustering approaches (STRUCTURE and POPS) that allow predicting the effects of future climatic changes on the population genetic structure of A. occidentale. We identified distinct genetic groups corresponding to the southwestern, central, and northern regions of the species' range. The characterized genetic clusters will disappear under future climate change scenarios, leading to a homogenization of genetic variability across the landscape. Our findings suggest a high likelihood for the loss of genetic diversity, which in turn will reduce the evolutionary potential of the species to cope with predicted future climatic changes. Results from this study may help develop management strategies to conserve the genetic diversity and structure of natural cashew populations.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":" ","pages":"357-367"},"PeriodicalIF":1.5,"publicationDate":"2023-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"71434930","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}