Ecological genetics最新文献

{"title":"Transgenesis in microalga Chlamydomonas reinhardtii: current approaches","authors":"Pavel A. Virolainen, Elena M. Chekunova","doi":"10.17816/ecogen624418","DOIUrl":"https://doi.org/10.17816/ecogen624418","url":null,"abstract":"Microalgae are a rich source of biologically active substances of natural origin, which have potential for use in pharmaceutical, agricultural, food and industrial production. Genetic engineering of microalgae opens up great prospects for creating improved strains that produce various food additives, commercial enzymes, as well as proteins for therapeutic purposes – antibodies, hormones and vaccines. Chlamydomonas reinhardtii P.A.Dang. is a unicellular green alga, a reference organism for studying the genetics of photosynthesis and developing new genetic engineering approaches in microalgae. The advantages of C. reinhardtii include the ability to transform all three of its genomes (nuclear, mitochondrial and chloroplast), low cost and ease of cultivation, safety for humans and the presence of a system for post-translational modification of proteins, which makes this organism a potential platform for use in biotechnology. Over the past few years, significant advances have been made in transgenesis of C. reinhardtii, including the use of new techniques based on the CRISPR/Cas9 genome editing technology. In this review, we summarize the available information on current approaches to transgenesis of the unicellular green alga C. reinhardtii: 1) general principles of transgenic constructs design for transformation of the nuclear and chloroplast genome, 2) popular selection markers used, 3) methods of cell transformation, 4) methods of genome editing using the CRISPR/Cas9 system.","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"34 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140455785","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The homeodomain of the Raphanus sativus WOX4 binds to the promoter of the LOG3 cytokinin biosynthesis gene","authors":"Xenia Andreevna Kuznetsova, I. Dodueva, L. A. Lutova","doi":"10.17816/ecogen624893","DOIUrl":"https://doi.org/10.17816/ecogen624893","url":null,"abstract":"Background \u0000The WOX4 transcription factor plays a crucial role in maintaining the organisation of cambium meristem during secondary growth, but its direct targets are unknown. The objectives of our work were to study the effect of WOX4 overexpression on the root development and gene expression in radish (Raphanus sativus L.), a root crop related to Arabidopsis thaliana, and to search for direct targets of the WOX4 in radish. \u0000Materials and methods \u0000Radish line 19 of the St. Petersburg State University radish genetic collection was used. Plants were grown on Murashige-Skoog medium and then in soil at 23оС and 16 h of daylight. Total DNA was extracted from radish seedlings using the CTAB method. The PCR-amplified full-length RsWOX4-2 gene, gene fragments or homeobox sequence were cloned into the vectors for overexpression (pB7WG2D), RNA interference (pH7GWIWG2) and yeast one-hybrid assay (pDEST22), respectively, using the Gateway system. The vectors for overexpression and RNA interference of RsWOX4-2 were transformed into Escherichia coli DH10B and then into Agrobacteium rhizogenes Arqua chemically competent cells. Radish seedlings were transformed transformation with A. rhizogenes containing vectors for overexpression and RNA interference of RsWOX4-2, and GUS-overexpressing A. rhizogenes was used as a control. Total RNA from transgenic radish roots was extracted with Trizol reagent. RNA reverse transcription was performed using dT-18 primers and RevertAid reverse transcriptase. qPCR was performed using the Eva Green reagent kit on a CFX96 thermocycler with fluorescence detection system. Results were processed using the 2-ΔΔCT method. \u0000Yeast transformation with competent Saccharomyces cerevisiae of Y2H Gold strain cells and yeast one-hybrid assay were performed as described in the article. The obtained yeast colonies transformed with plasmids containing TF homeodomain sequence and promoter regions of genes were grown on DDO and TDO selective media with different concentrations of 3-amino-1,2,4-triazole. \u0000Statistical processing based on Student's t-test and graphing were performed using the ggplot2 package for the R programming language (v.4.0.2). \u0000Results \u0000Overexpression of the RsWOX4-2 gene affects the structure of the radish root stele and alters the number of vessels and cambium cells. Overexpression and RNA interference of the RsWOX4-2 causes changes in the expression levels of putative target genes with the WOX family transcription factor conserved binding sites in their promoters. Using the yeast one-hybrid assay, we have shown that the DNA-binding homeodomain of RsWOX4-2 interacts with the TAATCC site in the promoter of the RsLOG3 gene, which encodes the enzyme for cytokinin biosynthesis. \u0000Conclusion \u0000We have demonstrated the effect of RsWOX4-2 overexpression on radish root stele and gene expression and identified the RsLOG3 as the putative direct target of the WOX4 transcription factor in radish.","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"81 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-01-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140505132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Metabolite profiling of leaves of three Ranunculus species","authors":"Pavel D. Smirnov, R. Puzanskiy, Sergey A. Vanisov, Maksim D. Dubrovskiy, A. Shavarda, M. Shishova, V. Yemelyanov","doi":"10.17816/ecogen623592","DOIUrl":"https://doi.org/10.17816/ecogen623592","url":null,"abstract":"BACKGROUND: Plants ability to survive oxygen deficiency is associated with the presence of various adaptations, majority of which are mediated by significant changes of metabolism. These alterations allow resistant wetland plants to grow even in an oxygen-depleted environment. AIM: To compare metabolic profiles of the leaves of the wetland species Ranunculus lingua, R. repens and R. sceleratus, and the mesophyte species R. acris growing in their natural habitat in order to identify the most characteristic metabolic traits of hypoxia-resistant plants. MATERIALS AND METHODS: Metabolite profiling was performed by GC-MS. Statistical analysis of metabolomics data was processed using R 4.3.1 Beagle Scouts. RESULTS: The resulting profile included 360 compounds. 74 of these were identified and 114 compounds were determined to a class. Sugars (114) were the most widely represented in the obtained profiles. 10 amino and 23 carboxylic acids, lipids and phenolic compounds have been identified. Significant differences were revealed between the profiles of leaf metabolomes of all tested species, which were clustered according to phylogenetic relation. The hydrophytic R. sceleratus, growing under submergence, showed the most unique metabolome, in which the level of sugars was reduced and intermediates of anaerobic metabolism, nitrogen metabolism, and alternative pathways of NAD(P)H reoxidation were accumulated. The profile of mesophytic R. acris was markedly different by reduced levels of amino acids, fatty acids and sterols. The metabolite profiles of waterlogged hydrophytes R. lingua and R. repens occupied an intermediate position. CONCLUSIONS: The identified differences of metabolomes of Ranunculus species are due to genetic determinants (life-form and adaptation strategy), ecological niche (biotope) and direct impact of a stressor (flooding).","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"66 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139213078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Analysis of arctic char (Salvelinus alpinus) haplotypes in the largest lakes of the North-West region of Russia for genetic monitoring","authors":"Vasily Golotin, Marina N. Kiseleva, Mitryushkina K. Diana, T. Filatova, Konstantin Rozhkovan, Anastasia E. Mamaeva, Olga V. Apalikova, Alina Zhukova","doi":"10.17816/ecogen622885","DOIUrl":"https://doi.org/10.17816/ecogen622885","url":null,"abstract":"Background. Arctic char is a residential form of the Arctic char Salvelinus alpinus and a commercial target in Ladoga Lake. Caused by fishing the gradual decline in the number of ones in the largest lakes of the North-Western region of Russia is compensated by measures for its artificial reproduction. The aim of this work was to carry out gaplotyping of the arctic char (Salvelinus alpinus) population in the largest lakes of the northwestern region of Russia. Materials and methods. The gaplotyping by PCR amplification in combination with restriction fragment length polymorphism (PCR-RFLP) of several amplified mtDNA regions, sequencing of the D-loop of mtDNA. Results. Screening studies of the genetic diversity of arctic char were carried out in three geographical population of the North-Western region of Russia and also the lake form of Arctic char from Sobachye Lake (Putorana Plateau, Western Siberia). The variability of a significant part (more than 35%) of the mitochondrial genome was analyzed including the regions of 16S rRNA/ND1/ND2 (2000 bp), COXI (567 bp), ND5/ND6 (2490 bp) and D-loop (1097 bp). Analysis of the nucleotide sequences of the control region mtDNA revealed 6 different haplotypes that were included in a single Eurasian group of char. Conclusion. The panel of PCR-RFLP markers can serve as a tool for monitoring the genetic structure of the arctic char populations of Ladoga Lake under conditions of ones artificial maintenance. Key words: arctic char, Salvelinus alpinus, mitochondrial DNA, PCR, RFLP, sequencing, haplotype","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"30 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139241751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Genetic Diversity and Autozygosity Estimates in Wild European Boars and Domesticated Pigs","authors":"S. Y. Bakoev, T. Romanets, A. V. Korobeynikova, A. I. Mishina, M. Kolosova, E. Romanets, Anatoly Yurievich Kolosov, L. Getmantseva","doi":"10.17816/ecogen569181","DOIUrl":"https://doi.org/10.17816/ecogen569181","url":null,"abstract":"Pigs are one of the most widely distributed domestic animals. The study of their genetic diversity and selection loci is of great interest both in the field of genetics and animal breeding, and in the aspect of conservation and development of breeding resources and food security. The aim of the presented work is to evaluate the autozygosity and distribution of autozygosity segments (HBD) in wild boars and pigs of the main commercial breeds: Large White, Landrace and Duroc, and to search for selection loci related to adaptation to habitat conditions and selection pressure. Based on the results of the genome scan, the average autozygosity values in boars and pigs were in the range of 0.23 - 0.29, but in boars about 0.08 of the genome share is covered by HBD segments, presumably originating from ancestors who lived about 206 years ago; in pigs - originating from ancestors who lived about 64 years ago. Only 3 segments met the criteria for top-HBD (frequency of at least 60% and at least 10 SNPs) in boars. In Large White, Landrace and Duroc pigs, 18, 9 and 35 segments were identified, respectively. In general, the analysis of HBD segments showed that they reflect the main breeding strategies aimed at developing commercial pigs.","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"59 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139250034","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Review of heterozygosity visualization approaches in the context of conservation research","authors":"Andrey A. Tomarovsky, A. Totikov, Aliya R. Yakupova, A. Graphodatsky, Sergei F. Kliver","doi":"10.17816/ecogen609552","DOIUrl":"https://doi.org/10.17816/ecogen609552","url":null,"abstract":"Estimating heterozygosity levels is one of the key metrics in conservation biology, as it contributes to the correct design of conservation programs for endangered species. With the development of full-genome sequencing technologies, it is now possible to more accurately estimate heterozygosity not only at the organismal level, but also at the population and species level. Modern conservation studies involve the processing of large volumes of full-genomic data, which leads to problems of interpretation and necessitates the study of modern visualization methods for clear and correct presentation of results. In this review, we elaborate on the main types of visualization of heterozygosity level estimates obtained using different approaches. We detail the theory behind each visualization method and discuss their features using examples from studies of non-model species with different conservation status. The review provides insight into the current tools for estimating and subsequently visualizing heterozygosity, as well as current trends in the field.","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"137 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139249037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Differential effect of estrogen and progesterone on in vitro growth of uterine leiomyoma cells with chromosome 7 deletions","authors":"A. S. Koltsova, O. Efimova, Vladislav S. Baranov, M. Yarmolinskaya, Nikolay I. Polenov, A. Pendina","doi":"10.17816/ecogen606642","DOIUrl":"https://doi.org/10.17816/ecogen606642","url":null,"abstract":"Background: The studies on how sex steroid hormones affect growth of uterine leiomyoma (UL) cells with chromosomal abnormalities is highly relevant for development of personalized tumor therapy. Aim: To study in vitro the isolated and combined effects of estrogen and progesterone on UL cells with chromosomal aberrations deletions in 7q. Materials and Methods: The study was performed on 15 ULs, excised from 15 women of 26-44 years of age who were not treated with hormones. UL cells were cultured in hormone-free medium, in the medium supplemented with estrogen, progesterone or both hormones. The chromosome preparations were made and stained with QFH/AcD to perform conventional karyotyping and fluorescence in situ hybridization (FISH) to accurately describe chromosomal rearrangements. The frequency of UL cells with chromosomal aberrations was assessed by interphase FISH. Results: Deletions in 7q were identified in 6 out of 15 karyotyped ULs; four of them had one clone with deletion in 7q whereas two others comprised two clones with 7q deletions of different length. The frequency of cells carrying deletions in 7q greatly varied in UL samples cultured in hormone-free medium: from 3.5 to 93.6 %. Exposure of cell cultures to estrogen and progesterone resulted in a fold change frequency increase in some of the ULs and decrease in the others. The most significant changes in the frequency of cells with deletions in 7q were registered in response to the isolated estrogen and, to a lesser extent, to progesterone exposure; less significant changes were observed after combined hormonal effect. Conclusions: In ULs with deletions in 7q, the frequency of abnormal cells may either increase or decrease in response to estrogen and progesterone in vitro supplementation. The isolated effect of estrogen or progesterone on the frequency of UL cells with deletion in 7q is more pronounced compared to the combined one.","PeriodicalId":502283,"journal":{"name":"Ecological genetics","volume":"71 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"139258560","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}