Genetica最新文献

{"title":"Comparative analysis of cold-responsive genes under short-term cold stimulation and cold-adaptive genes under long-term heterogeneous environments reveals a cold adaptation mechanism in weeping forsythia.","authors":"Yong Li,&nbsp;Shu-Chen Wang,&nbsp;Qian Li,&nbsp;Ming-Wan Li,&nbsp;Run-Li Mao,&nbsp;He-Chen Zhang,&nbsp;Wang-Jun Yuan,&nbsp;Jine Quan","doi":"10.1007/s10709-022-00176-4","DOIUrl":"https://doi.org/10.1007/s10709-022-00176-4","url":null,"abstract":"<p><p>Identifying cold-related genes can provide insights into the cold adaptation mechanism of weeping forsythia. In this study, we compared the changes in gene expressions and physiological and biochemical indices under short-term cold stimulation with the changes in gene sequences under a long-term heterogeneous environment to investigate the cold adaptation mechanism in weeping forsythia. The data of adaptive gene sequence changes, e.g., single nucleotide polymorphisms, were obtained from previous landscape genomics studies. The physiological and biochemical indicators and transcriptome results showed that weeping forsythia initiated a series of programs, including increasing cell osmotic pressures, scavenging ROS, activating the defense mechanism that crosses with pathogen infection, and upregulating CBF/DREB1 transcription factor 1, to cope with short-term cold stress. A reanalysis of landscape genomic data suggested that weeping forsythia responded to long-term heterogeneous cold stress by the differentiation of genes related to synthesis of aromatic substances and adenosine triphosphate. Our results supported the hypothesis that the adaptation mechanisms of species to short-term environmental stimulation and long-term stress in heterogeneous environments are different. The differences in cold tolerance among populations are not necessarily obtained by changing cold-responsive gene sequences. This study provides new insights into the cold adaptation mechanisms of plants.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"151 1","pages":"47-59"},"PeriodicalIF":1.5,"publicationDate":"2023-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9190467","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, molecular characterization, and in silico structural analysis of larval salivary glands Netrin-A as a potent biomarker from Lucilia sericata (Diptera: Calliphoridae).","authors":"Masoumeh Bagheri,&nbsp;Hamzeh Alipour,&nbsp;Tahereh Karamzadeh,&nbsp;Marzieh Shahriari-Namadi,&nbsp;Abbasali Raz,&nbsp;Kourosh Azizi,&nbsp;Javad Dadgar Pakdel,&nbsp;Mohammad Djaefar Moemenbellah-Fard","doi":"10.1007/s10709-022-00164-8","DOIUrl":"https://doi.org/10.1007/s10709-022-00164-8","url":null,"abstract":"<p><p>The greenbottle blowfly Lucilia sericata (L. sericata) is increasingly used in larval therapy of chronic wounds. Netrins as bifunctional proteins are in the superfamily of Laminins secreted from larval salivary glands. The Netrin protein has a significant instructive role in axon guidance, causing neuronal outgrowth, angiogenesis, and cell migration. It seems to be crucial in wound healing and acts as a potential biomarker in diagnosing some clinical diseases. This survey aimed to identify molecular features and analyze in silico structural configuration of Netrin-A in L. sericata larvae. The larvae were reared under standard maggotarium conditions. The nucleic acid sequence of L. sericata Netrin-A (LSN-A) was then identified using rapid amplification of circular DNA ends (RACE) and rapid amplification of genomic ends (RAGE). Parts of the Netrin-A gene, including the middle, 3'-, and 5'-ends, were identified, TA cloned in pTG19 plasmid, and transferred into DH5ɑ Escherichia coli. Each part was sequenced and assembled using SeqMan software. This gene structure was further subjected to in silico analysis. The DNA of LSN-A was identified to be 2407 bp, while its mRNA sequence was recognized as 2115 bp by Oligo0.7 software. It translated the Netrin-A protein with 704 amino acid residues. Its estimated molecular weight was 78.6 kDa. Sequencing of this fragment and its BLAST analysis revealed laminin-based high (95%) similarity with the mRNA sequence of Lucilia cuprina Netrin-A. The 3-D structure of Netrin-A drawn by SWISS-MODEL exhibited its partial resemblance to the reference molecule Netrin-1 of Homo sapiens. This study supports the molecular and structural analyses of LSN-A protein, which could lead to wound treatment. Ultimately, it can be an effective candidate to ameliorate injury. Our next attempt is to produce LSN-A recombinant protein for use in biomedical sciences.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"379-394"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33469985","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 structure of Enyalius capetinga (Squamata, Leiosauridae) in Central Cerrado and transitional areas between the Cerrado and the Atlantic forest, with updated geographic distribution.","authors":"M A Ishihara,&nbsp;F M C B Domingos,&nbsp;S C Gomides,&nbsp;I A Novelli,&nbsp;G R Colli,&nbsp;S M Vargas","doi":"10.1007/s10709-022-00170-w","DOIUrl":"https://doi.org/10.1007/s10709-022-00170-w","url":null,"abstract":"<p><p>The Brazilian Cerrado is considered a biodiversity hotspot highly threatened by human activities. Recently, many studies have demonstrated how underestimated is Cerrado's biodiversity considering squamate species, and the identification of divergent and cryptic lineages is essential for the formulation of effective conservation strategies. The transition areas between the Cerrado and the Atlantic Forest are even less known and, consequently, often dismissed in conservation policies. As previous studies suggested the presence of cryptic diversity within E. capetinga, we investigated patterns and processes in the geographic distribution of its genealogical lineages. We used DNA sequences from individuals collected in six localities and sequences publicly available from three mitochondrial markers (CYT-B, 16S and ND4) and one nuclear marker (C-Mos). We tested if the core and ecotone regions of the Cerrado show differences in biotic and abiotic characteristics that could promote genetic structure and divergence among lineages within E. capetinga. We found evidence for divergent lineages within the species, but not congruent with our hypothesis. Similar divergent patterns were observed in other Cerrado lizards, including interspecific divergences within the Enyalius genus. Molecular characterization of field-collected individuals (previously identified as E. bilineatus), allowed us to update the geographic distribution of the species to include the ecotone between the Cerrado and the Atlantic Forest, an area where species distribution overlap.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"367-377"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33506365","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":"Long-term evolution of quantitative traits in the Drosophila melanogaster species subgroup.","authors":"Amir Yassin,&nbsp;Nelly Gidaszewski,&nbsp;Vincent Debat,&nbsp;Jean R David","doi":"10.1007/s10709-022-00171-9","DOIUrl":"https://doi.org/10.1007/s10709-022-00171-9","url":null,"abstract":"<p><p>Quantitative genetics aims at untangling the genetic and environmental effects on phenotypic variation. Trait heritability, which summarizes the relative importance of genetic effects, is estimated at the intraspecific level, but theory predicts that heritability could influence long-term evolution of quantitative traits. The phylogenetic signal concept bears resemblance to heritability and it has often been called species-level heritability. Under certain conditions, such as trait neutrality or contribution to phylogenesis, within-species heritability and between-species phylogenetic signal should be correlated. Here, we investigate the potential relationship between these two concepts by examining the evolution of multiple morphological traits for which heritability has been estimated in Drosophila melanogaster. Specifically, we analysed 42 morphological traits in both sexes on a phylogeny inferred from 22 nuclear genes for nine species of the melanogaster subgroup. We used Pagel's λ as a measurement of phylogenetic signal because it is the least influenced by the number of analysed taxa. Pigmentation traits showed the strongest concordance with the phylogeny, but no correlation was found between phylogenetic signal and heritability estimates mined from the literature. We obtained data for multiple climatic variables inferred from the geographical distribution of each species. Phylogenetic regression of quantitative traits on climatic variables showed a significantly positive correlation with heritability. Convergent selection, the response to which depends on the trait heritability, may have led to the null association between phylogenetic signal and heritability for morphological traits in Drosophila. We discuss the possible causes of discrepancy between both statistics and caution against their confusion in evolutionary biology.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 6","pages":"343-353"},"PeriodicalIF":1.5,"publicationDate":"2022-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33512044","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 microsatellites in coding regions provides insights into the adaptability of the giant panda, polar bear and brown bear","authors":"Meiling Cheng, Daxin Xie, Megan Price, Chuang Zhou, Xiuyue Zhang","doi":"10.1007/s10709-022-00173-7","DOIUrl":"https://doi.org/10.1007/s10709-022-00173-7","url":null,"abstract":"","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 1","pages":"355 - 366"},"PeriodicalIF":1.5,"publicationDate":"2022-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48797236","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":"Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia).","authors":"Didier Aurelle,&nbsp;Marine Pratlong,&nbsp;Nicolas Oury,&nbsp;Anne Haguenauer,&nbsp;Pauline Gélin,&nbsp;Hélène Magalon,&nbsp;Mehdi Adjeroud,&nbsp;Pascal Romans,&nbsp;Jeremie Vidal-Dupiol,&nbsp;Michel Claereboudt,&nbsp;Camille Noûs,&nbsp;Lauric Reynes,&nbsp;Eve Toulza,&nbsp;François Bonhomme,&nbsp;Guillaume Mitta,&nbsp;Pierre Pontarotti","doi":"10.1007/s10709-022-00165-7","DOIUrl":"https://doi.org/10.1007/s10709-022-00165-7","url":null,"abstract":"<p><p>Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 5","pages":"247-262"},"PeriodicalIF":1.5,"publicationDate":"2022-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33455552","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":"Epimutations and mutations, nurturing phenotypic diversity.","authors":"Jasmine M Shah","doi":"10.1007/s10709-021-00124-8","DOIUrl":"https://doi.org/10.1007/s10709-021-00124-8","url":null,"abstract":"<p><p>Epimutations and mutations are two dissimilar mechanisms that have contributed to the phenotypic diversities in organisms. Though dissimilar, many previous studies have revealed that the consequences of epimutations and mutations are not mutually exclusive. DNA rich in epigenetic modifications can be prone to mutations and vice versa. In order to get a better insight into the molecular evolution in organisms, it is important to consider the information of both genetic and epigenetic changes in their genomes. Understanding the similarities and differences between the consequences of epimutations and mutations is required for a better interpretation of phenotypic diversities in organisms. Factors contributing to epigenetic changes such as paramutations and mutation hotspots and, the correlation of the interdependence of mutations and epigenetic changes in DNA are important aspects that need to be considered for molecular evolutionary studies. Thus, this review explains what epimutations are, their causes, how they are similar/different from mutations, and the influence of epigenetic changes and mutations on each other, further emphasizing how molecular evolution involving both mutations and epimutations can lead to speciation. Considering this approach will aid in reorganizing taxonomic classifications, importantly, solving disparities in species identification.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 3-4","pages":"171-181"},"PeriodicalIF":1.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1007/s10709-021-00124-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39015510","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":"What is a phenotype? History and new developments of the concept.","authors":"Dominique de Vienne","doi":"10.1007/s10709-021-00134-6","DOIUrl":"10.1007/s10709-021-00134-6","url":null,"abstract":"<p><p>Even though the word \"phenotype\", as well as the expression \"genotype-phenotype relationship\", are a part of the everyday language of biologists, they remain abstract notions that are sometimes misunderstood or misused. In this article, I begin with a review of  the genesis of the concept of phenotype and of the meaning of the genotype-phenotype \"relationship\" from a historical perspective. I then illustrate how the development of new approaches for exploring the living world has enabled us to phenotype organisms at multiple levels, with traits that can either be measures or parameters of functions, leading to a virtually unlimited amount of phenotypic data. Thus, pleiotropy becomes a central issue in the study of the genotype-phenotype relationship. Finally, I provide a few examples showing that important genetic and evolutionary features clearly differ with the phenotypic level considered. The way genotypic variation propagates across the phenotypic levels to shape fitness variation is an essential research program in biology.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 3-4","pages":"153-158"},"PeriodicalIF":1.3,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39859840","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":"Heritability: What's the point? What is it not for? A human genetics perspective.","authors":"Nicolas Robette,&nbsp;Emmanuelle Génin,&nbsp;Françoise Clerget-Darpoux","doi":"10.1007/s10709-022-00149-7","DOIUrl":"https://doi.org/10.1007/s10709-022-00149-7","url":null,"abstract":"<p><p>In this paper, we explain the concept of heritability and describe the different methods and the genotype-phenotype correspondences used to estimate heritability in the specific field of human genetics. Heritability studies are conducted on extremely diverse human traits: quantitative traits (physical, biological, but also cognitive and behavioral measurements) and binary traits (as is the case of most human diseases). Instead of variables such as education and socio-economic status as covariates in genetic studies, they are now the direct object of genetic analysis. We make a review of the different assumptions underlying heritability estimates and dispute the validity of most of them. Moreover, and maybe more importantly, we show that they are very often misinterpreted. These erroneous interpretations lead to a vision of a genetic determinism of human traits. This vision is currently being widely disseminated not only by the mass media and the mainstream press, but also by the scientific press. We caution against the dangerous implication it has both medically and socially. Contrarily to the field of animal and plant genetics for which the polygenic model and the concept of heritability revolutionized selection methods, we explain why it does not provide answer in human genetics.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 3-4","pages":"199-208"},"PeriodicalIF":1.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39731666","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":"Associating complex traits with genetic variants: polygenic risk scores, pleiotropy and endophenotypes.","authors":"Gene S Fisch","doi":"10.1007/s10709-021-00138-2","DOIUrl":"https://doi.org/10.1007/s10709-021-00138-2","url":null,"abstract":"<p><p>Genotype-phenotype causal modeling has evolved significantly since Johannsen's and Wright's original designs were published. The development of genomewide assays to interrogate and detect possible causal variants associated with complex traits has expanded the scope of genotype-phenotype research considerably. Clusters of causal variants discovered by genomewide assays and associated with complex traits have been used to develop polygenic risk scores to predict clinical diagnoses of multidimensional human disorders. However, genomewide investigations have met with many challenges to their research designs and statistical complexities which have hindered the reliability and validity of their predictions. Findings linked to differences in heritability estimates between causal clusters and complex traits among unrelated individuals remain a research area of some controversy. Causal models developed from case-control studies as opposed to experiments, as well as other issues concerning the genotype-phenotype causal model and the extent to which various forms of pleiotropy and the concept of the endophenotype add to its complexity, will be reviewed.</p>","PeriodicalId":55121,"journal":{"name":"Genetica","volume":"150 3-4","pages":"183-197"},"PeriodicalIF":1.5,"publicationDate":"2022-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39540455","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}