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Felberg A, Bieńkowski M, Stokowy T, Myszczyński K, Polakiewicz Z, Kitowska K, Sądej R, Mohlin F, Kuźniewska A, Kowalska D, Stasiłojć G, Jongerius I, Spaapen R, Mesa-Guzman M, Montuenga LM, Blom AM, Pio R, Okrój M. Elevated expression of complement factor I in lung cancer cells associates with shorter survival-Potentially via non-canonical mechanism. Transl Res 2024:S1931-5244(24)00033-1. [PMID: 38395390 DOI: 10.1016/j.trsl.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 01/27/2024] [Accepted: 02/20/2024] [Indexed: 02/25/2024]
Abstract
While numerous membrane-bound complement inhibitors protect the body's cells from innate immunity's autoaggression, soluble inhibitors like complement factor I (FI) are rarely produced outside the liver. Previously, we reported the expression of FI in non-small cell lung cancer (NSCLC) cell lines. Now, we assessed the content of FI in cancer biopsies from lung cancer patients and associated the results with clinicopathological characteristics and clinical outcomes. Immunohistochemical staining intensity did not correlate with age, smoking status, tumor size, stage, differentiation grade, and T cell infiltrates, but was associated with progression-free survival (PFS), overall survival (OS) and disease-specific survival (DSS). Multivariate Cox analysis of low vs. high FI content revealed HR 0.55, 95 % CI 0.32-0.95, p=0.031 for PFS, HR 0.51, 95 % CI 0.25-1.02, p=0.055 for OS, and HR 0.32, 95 % CI 0.12-0.84, p=0.021 for DSS. Unfavorable prognosis might stem from the non-canonical role of FI, as the staining pattern did not correlate with C4d - the product of FI-supported degradation of active complement component C4b. To elucidate that, we engineered three human NSCLC cell lines naturally expressing FI with CRISPR/Cas9 technology, and compared the transcriptome of FI-deficient and FI-sufficient clones in each cell line. RNA sequencing revealed differentially expressed genes engaged in intracellular signaling pathways controlling proliferation, apoptosis, and responsiveness to growth factors. Moreover, in vitro colony-formation assays showed that FI-deficient cells formed smaller foci than FI-sufficient NSCLC cells, but their size increased when purified FI protein was added to the medium. We postulate that a non-canonical activity of FI influences cellular physiology and contributes to the poor prognosis of lung cancer patients.
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Affiliation(s)
- Anna Felberg
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1 street, 80-211 Gdańsk, Poland
| | | | - Tomasz Stokowy
- Scientific Computing Group, IT Division, University of Bergen, Norway
| | - Kamil Myszczyński
- Centre of Biostatistics and Bioinformatics Analysis, Medical University of Gdańsk, Poland
| | - Zuzanna Polakiewicz
- Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Poland
| | - Kamila Kitowska
- Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Poland
| | - Rafał Sądej
- Department of Molecular Enzymology and Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Poland
| | - Frida Mohlin
- Department of Translational Medicine, Lund University, Sweden
| | - Alicja Kuźniewska
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1 street, 80-211 Gdańsk, Poland
| | - Daria Kowalska
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1 street, 80-211 Gdańsk, Poland
| | - Grzegorz Stasiłojć
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1 street, 80-211 Gdańsk, Poland
| | - Ilse Jongerius
- Department of Immunopathology, Sanquin Research, Amsterdam and Landsteiner Laboratory, Amsterdam University Medical Center, University of Amsterdam, The Netherlands; Emma Children's Hospital, Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam University Medical Center, The Netherlands
| | - Robbert Spaapen
- Emma Children's Hospital, Department of Pediatric Immunology, Rheumatology and Infectious Diseases, Amsterdam University Medical Center, The Netherlands
| | - Miguel Mesa-Guzman
- Department of Thoracic Surgery, Clinica Universidad de Navarra, Pamplona, Spain
| | - Luis M Montuenga
- Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain; Program in Solid Tumors, Cima Universidad de Navarra, Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain
| | - Anna M Blom
- Department of Translational Medicine, Lund University, Sweden
| | - Ruben Pio
- Program in Solid Tumors, Cima Universidad de Navarra, Cancer Center Clinica Universidad de Navarra (CCUN), Pamplona, Spain; Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain; Instituto de Investigación Sanitaria de Navarra (IdisNa), Pamplona, Spain; Department of Biochemistry and Genetics, School of Sciences, University of Navarra, Pamplona, Spain
| | - Marcin Okrój
- Department of Cell Biology and Immunology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1 street, 80-211 Gdańsk, Poland.
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Nowak JI, Olszewska AM, Piotrowska A, Myszczyński K, Domżalski P, Żmijewski MA. PDIA3 modulates genomic response to 1,25-dihydroxyvitamin D 3 in squamous cell carcinoma of the skin. Steroids 2023; 199:109288. [PMID: 37549780 DOI: 10.1016/j.steroids.2023.109288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 07/28/2023] [Accepted: 08/02/2023] [Indexed: 08/09/2023]
Abstract
An active form of vitamin D3 (1,25-dihydroxyvitamin D3) acts through vitamin D receptor (VDR) initiating genomic response, but several studies described also non-genomic actions of 1,25-dihydroxyvitamin D3, implying the role of PDIA3 in the process. PDIA3 is a membrane-associated disulfide isomerase involved in disulfide bond formation, protein folding, and remodeling. Here, we used a transcriptome-based approach to identify changes in expression profiles in PDIA3-deficient squamous cell carcinoma line A431 after 1,25-dihydroxyvitamin D3 treatment. PDIA3 knockout led to changes in the expression of more than 2000 genes and modulated proliferation, cell cycle, and mobility of cells; suggesting an important regulatory role of PDIA3. PDIA3-deficient cells showed increased sensitivity to 1,25-dihydroxyvitamin D3, which led to decrease migration. 1,25-dihydroxyvitamin D3 treatment altered also genes expression profile of A431ΔPDIA3 in comparison to A431WT cells, indicating the existence of PDIA3-dependent genes. Interestingly, classic targets of VDR, including CAMP (Cathelicidin Antimicrobial Peptide), TRPV6 (Transient Receptor Potential Cation Channel Subfamily V Member 6), were regulated differently by 1,25-dihydroxyvitamin D3, in A431ΔPDIA3. Deletion of PDIA3 impaired 1,25-dihydroxyvitamin D3-response of genes, such as PTGS2, MMP12, and FOCAD, which were identified as PDIA3-dependent. Additionally, response to 1,25-dihydroxyvitamin D3 in cancerous A431 cells differed from immortalized HaCaT keratinocytes, used as non-cancerous control. Finally, silencing of PDIA3 and 1,25-dihydroxyvitamin D3, at least partially reverse the expression of cancer-related genes in A431 cells, thus targeting PDIA3 and use of 1,25-dihydroxyvitamin D3 could be considered in a prevention and therapy of the skin cancer. Taken together, PDIA3 has a strong impact on gene expression and physiology, including genomic response to 1,25-dihydroxyvitamin D3.
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Affiliation(s)
- Joanna I Nowak
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Anna M Olszewska
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Anna Piotrowska
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Kamil Myszczyński
- Centre of Biostatistics and Bioinformatics Analysis Medical University of Gdansk, 1a Debinki, 80-211 Gdansk, Poland.
| | - Paweł Domżalski
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
| | - Michał A Żmijewski
- Department of Histology, Medical University of Gdansk, 1a Dębinki, 80-211 Gdansk, Poland.
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Fotschki B, Ognik K, Cholewińska E, Grzelak-Błaszczyk K, Myszczyński K, Krauze M, Juśkiewicz J. Effect of Chromium Nanoparticles and Switching from a High-Fat to a Low-Fat Diet on the Cecal Microenvironment in Obese Rats. Nutrients 2023; 15:3118. [PMID: 37513536 PMCID: PMC10384463 DOI: 10.3390/nu15143118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 07/09/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Previous studies showed that chromium nanoparticles (Cr-NPs) might be used as dietary compounds against some obesity-related disorders; however, there is little information on how these compounds influence the gut microenvironment. The aim of this study was to investigate whether the negative effects of a high-fat diet in the large intestine of rats might be mitigated by switching to a low-fat diet and supplementation with Cr-NPs. Microbiota sequencing analysis revealed that the main action of the Cr-NPs was focused on changing the gut microbiota's activity. Supplementation with nanoparticles decreased the activity of β-glucuronidase and enzymes responsible for the hydrolysis of dietary oligosaccharides and, thus, lowered the concentration of short-chain fatty acids in the cecum. In this group, there was also an elevated level of cecal lithocholic acid. The most favorable effect on the regulation of obesity-related disorders was observed when a high-fat diet was switched to a low-fat diet. This dietary change enhanced the production of short-chain fatty acids, reduced the level of secondary bile acids, and increased the microbial taxonomic richness, microbial differences, and microbial enzymatic activity in the cecum. To conclude, supplementation of a high-fat diet with Cr-NPs primarily had an effect on intestinal microbial activity, but switching to a low-fat diet had a powerful, all-encompassing effect on the gut that improved both microbial activity and composition.
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Affiliation(s)
- Bartosz Fotschki
- Division of Food Science, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Katarzyna Ognik
- Department of Biochemistry and Toxicology, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Ewelina Cholewińska
- Department of Biochemistry and Toxicology, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Katarzyna Grzelak-Błaszczyk
- Institute of Food Technology and Analysis, Lodz University of Technology, Stefanowskiego 2/22, 90-537 Lodz, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Magdalena Krauze
- Department of Biochemistry and Toxicology, Faculty of Animal Sciences and Bioeconomy, University of Life Sciences in Lublin, Akademicka 13, 20-950 Lublin, Poland
| | - Jerzy Juśkiewicz
- Division of Food Science, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
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Krawczyk K, Myszczyński K, Nobis M, Sawicki J. Insights into adaptive evolution of plastomes in Stipa L. (Poaceae). BMC Plant Biol 2022; 22:525. [PMID: 36372890 PMCID: PMC9661759 DOI: 10.1186/s12870-022-03923-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 11/01/2022] [Indexed: 06/03/2023]
Abstract
BACKGROUND The study presents results of research on the evolution of plastid genomes in Stipa L. which is a large genus of the Poaceae family, comprising species diverse in terms of geographic distribution, growing under highly variated habitat conditions. Complete plastome sequences of 43 taxa from Stipeae and Ampelodesmae tribes were analyzed for the variability of the coding regions against the background of phylogenetic relationships within the genus Stipa. The research hypothesis put forward in our research was that some of coding regions are affected by a selection pressure differentiated between individual phylogenetic lines of Stipa, potentially reducing the phylogenetic informativeness of these CDS. The study aimed to answer the question, which genes evolve in Stipa most rapidly and what kind of changes in the properties of encoded amino acids this entails. Another goal of this research was to find out whether individual genes are affected by positive selection and finally, whether selective pressure is uniform within the genus or does it vary between particular evolutionary lines within the genus. RESULTS Results of our study proved the presence of selective pressure in 11 genes: ccsA, matK, ndhC, ndhF, ndhK, rbcL, rpoA rpoC1, rpoC2, rps8 and rps11. For the first time the effect of positive selection on the rps8, rps11, and ndhK genes was documented in grasses. The varied pace of evolution, different intensity and effects of selective pressure have been demonstrated between particular phylogenetic lines of the genus tested. CONCLUSIONS Positive selection in plastid genome in Stipa mostly affects photosynthetic genes. The potential strongest adaptive pressure was observed in the rbcL gene, especially in the oldest evolutionary group comprising Central Asian high-mountain species: S. basiplumosa, S. klimesii, S. penicillata and S. purpurea, where adaptive pressure probably affected the amino acids directly related to the efficiency of CO2 assimilation.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Kamil Myszczyński
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Gronostajowa 3, 30-387, Kraków, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland
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Fotschki B, Wiczkowski W, Sawicki T, Sójka M, Myszczyński K, Ognik K, Juśkiewicz J. Stimulation of the intestinal microbiota with prebiotics enhances hepatic levels of dietary polyphenolic compounds, lipid metabolism and antioxidant status in healthy rats. Food Res Int 2022; 160:111754. [DOI: 10.1016/j.foodres.2022.111754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 07/04/2022] [Accepted: 07/26/2022] [Indexed: 11/28/2022]
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Ciereszko A, Dietrich MA, Słowińska M, Nynca J, Ciborowski M, Kaczmarek MM, Myszczyński K, Kiśluk J, Majewska A, Michalska-Falkowska A, Kodzik N, Reszeć J, Sierko E, Nikliński J. Application of two-dimensional difference gel electrophoresis to identify protein changes between center, margin, and adjacent non-tumor tissues obtained from non-small-cell lung cancer with adenocarcinoma or squamous cell carcinoma subtype. PLoS One 2022; 17:e0268073. [PMID: 35512017 PMCID: PMC9071164 DOI: 10.1371/journal.pone.0268073] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 04/21/2022] [Indexed: 12/12/2022] Open
Abstract
Lung cancer is responsible for the most cancer-related mortality worldwide and the mechanism of its development is poorly understood. Proteomics has become a powerful tool offering vital knowledge related to cancer development. Using a two-dimensional difference gel electrophoresis (2D-DIGE) approach, we sought to compare tissue samples from non-small-cell lung cancer (NSCLC) patients taken from the tumor center and tumor margin. Two subtypes of NSCLC, adenocarcinoma (ADC) and squamous cell carcinoma (SCC) were compared. Data are available via ProteomeXchange with identifier PXD032736 and PXD032962 for ADC and SCC, respectively. For ADC proteins, 26 significant canonical pathways were identified, including Rho signaling pathways, a semaphorin neuronal repulsive signaling pathway, and epithelial adherens junction signaling. For SCC proteins, nine significant canonical pathways were identified, including hypoxia-inducible factor-1α signaling, thyroid hormone biosynthesis, and phagosome maturation. Proteins differentiating the tumor center and tumor margin were linked to cancer invasion and progression, including cell migration, adhesion and invasion, cytoskeletal structure, protein folding, anaerobic metabolism, tumor angiogenesis, EMC transition, epithelial adherens junctions, and inflammatory responses. In conclusion, we identified several proteins that are important for the better characterization of tumor development and molecular specificity of both lung cancer subtypes. We also identified proteins that may be important as biomarkers and/or targets for anticancer therapy.
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Affiliation(s)
- Andrzej Ciereszko
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
- * E-mail:
| | - Mariola A. Dietrich
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Mariola Słowińska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Nynca
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Michał Ciborowski
- Metabolomics Laboratory, Clinical Research Centre, Medical University of Bialystok, Bialystok, Poland
| | - Monika M. Kaczmarek
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Kiśluk
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
| | - Anna Majewska
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Natalia Kodzik
- Department of Gametes and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Joanna Reszeć
- Department of Medical Pathomorphology, Medical University of Bialystok, Bialystok, Poland
| | - Ewa Sierko
- Department of Oncology, Medical University of Bialystok, Bialystok, Poland
| | - Jacek Nikliński
- Department of Clinical Molecular Biology, Medical University of Bialystok, Bialystok, Poland
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Szandar K, Krawczyk K, Myszczyński K, Ślipiko M, Sawicki J, Szczecińska M. Breaking the limits - multichromosomal structure of an early eudicot Pulsatilla patens mitogenome reveals extensive RNA-editing, longest repeats and chloroplast derived regions among sequenced land plant mitogenomes. BMC Plant Biol 2022; 22:109. [PMID: 35264098 PMCID: PMC8905907 DOI: 10.1186/s12870-022-03492-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 02/25/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND The mitogenomes of vascular plants are one of the most structurally diverse molecules. In the present study we characterize mitogenomes of a rare and endangered species Pulsatilla patens. We investigated the gene content and its RNA editing potential, repeats distribution and plastid derived sequences. RESULTS The mitogenome structure of early divergent eudicot, endangered Pulsatilla patens does not support the master chromosome hypothesis, revealing the presence of three linear chromosomes of total length 986 613 bp. The molecules are shaped by the presence of extremely long, exceeding 87 kbp repeats and multiple chloroplast-derived regions including nearly complete inverted repeat. Since the plastid IR content of Ranunculales is very characteristic, the incorporation into mitogenome could be explained rather by intracellular transfer than mitochondrial HGT. The mitogenome contains almost a complete set of genes known from other vascular plants with exception of rps10 and sdh3, the latter being present but pseudogenized. Analysis of long ORFs enabled the identification of genes which are rarely present in plant mitogenomes, including RNA and DNA polymerases, albeit their presence even at species level is variable. Mitochondrial transcripts of P. patens were edited with a high frequency, which exceeded the level known in other analyzed angiosperms, despite the strict qualification criteria of counting the editing events and taking into analysis generally less frequently edited leaf transcriptome. The total number of edited sites was 902 and nad4 was identified as the most heavily edited gene with 65 C to U changes. Non-canonical, reverse U to C editing was not detected. Comparative analysis of mitochondrial genes of three Pulsatilla species revealed a level of variation comparable to chloroplast CDS dataset and much higher infrageneric differentiation than in other known angiosperm genera. The variation found in CDS of mitochondrial genes is comparable to values found among Pulsatilla plastomes. Despite the complicated mitogenome structure, 14 single copy regions of 329 kbp, not splitted by repeats or plastid-derived sequences (MTPT), revealed the potential for phylogenetic, phylogeographic and population genetics studies by revealing intra- and interspecific collinearity. CONCLUSIONS This study provides valuable new information about mitochondrial genome of early divergent eudicots, Pulsatilla patens, revealed multi-chromosomal structure and shed new light on mitogenomics of early eudicots.
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Affiliation(s)
- Kamil Szandar
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Kamil Myszczyński
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland.
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Monika Szczecińska
- Department of Ecology and Environmental Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 3, 10- 727, Olsztyn, Poland.
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Żelechowski M, Molcan T, Bilska K, Myszczyński K, Olszewski J, Karpiesiuk K, Wyrębek J, Kulik T. Patterns of Diversity of Fusarium Fungi Contaminating Soybean Grains. Toxins (Basel) 2021; 13:884. [PMID: 34941721 PMCID: PMC8706617 DOI: 10.3390/toxins13120884] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 11/16/2022] Open
Abstract
Soybean is an important, high protein source of food and feed. However, like other agricultural grains, soybean may pose a risk to human and animal health due to contamination of the grains with toxigenic Fusaria and associated mycotoxins. In this study, we investigated the diversity of Fusaria on a panel of 104 field isolates obtained from soybean grains during the growing seasons in 2017-2020. The results of species-specific PCR analyses showed that Fusarium avenaceum was the most common (n = 40) species associated with soybean grains in Poland, followed by F. equiseti (n = 22) and F. sporotrichioides (11 isolates). A set of isolates, which was not determined based on PCR analyses, was whole genome sequenced. Multiple sequence analyses using tef-1α, top1, rpb1, rpb2, tub2, pgk, cam and lsu genes showed that most of them belonged to Equiseti clade. Three cryptic species from this clade: F. clavum, F. flagelliforme and FIESC 31 (lacking Latin binomial) were found on soybean for the first time. This is the first report demonstrating the prevalence of Fusaria on soybean grains in Poland.
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Affiliation(s)
- Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.B.); (J.W.)
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Adolfa Pawińskiego 5A, 02-106 Warsaw, Poland;
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.B.); (J.W.)
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, 10-748 Olsztyn, Poland;
| | - Jacek Olszewski
- Experimental Education Unit, Oczapowskiego 8, 10-719 Olsztyn, Poland;
| | - Krzysztof Karpiesiuk
- Department of Pig Breeding, University of Warmia and Mazury in Olsztyn, ul. Oczapowskiego 5, 10-719 Olsztyn, Poland;
| | - Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.B.); (J.W.)
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland; (K.B.); (J.W.)
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Wyrębek J, Molcan T, Myszczyński K, van Diepeningen AD, Stakheev AA, Żelechowski M, Bilska K, Kulik T. Uncovering Diagnostic Value of Mitogenome for Identification of Cryptic Species Fusarium graminearum Sensu Stricto. Front Microbiol 2021; 12:714651. [PMID: 34531839 PMCID: PMC8439580 DOI: 10.3389/fmicb.2021.714651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
Fungal complexes are often composed of morphologically nearly indistinguishable species with high genetic similarity. However, despite their close relationship, they can exhibit distinct phenotypic differences in pathogenicity and production of mycotoxins. Many plant pathogenic and toxigenic fungi have been shown to consist of such cryptic species. Identification of cryptic species in economically important pathogens has added value in epidemiologic studies and provides opportunities for better control. Analysis of mitochondrial genomes or mitogenomics opens up dimensions for improved diagnostics of fungi, especially when efficient recovery of DNA is problematic. In comparison to nuclear DNA, mitochondrial DNA (mtDNA) can be amplified with improved efficacy due to its multi-copy nature. However, to date, only a few studies have demonstrated the usefulness of mtDNA for identification of cryptic species within fungal complexes. In this study, we explored the value of mtDNA for identification of one of the most important cereal pathogens Fusarium graminearum sensu stricto (F.g.). We found that homing endonucleases (HEGs), which are widely distributed in mitogenomes of fungi, display small indel polymorphism, proven to be potentially species specific. The resulting small differences in their lengths may facilitate further differentiation of F.g. from the other cryptic species belonging to F. graminearum species complex. We also explored the value of SNP analysis of the mitogenome for typing F.g. The success in identifying F.g. strains was estimated at 96%, making this tool an attractive complement to other techniques for identification of F.g.
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Affiliation(s)
- Joanna Wyrębek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Kamil Myszczyński
- Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | | | - Alexander A Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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10
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Ślipiko M, Myszczyński K, Buczkowska K, Bączkiewicz A, Szczecińska M, Sawicki J. Molecular delimitation of European leafy liverworts of the genus Calypogeia based on plastid super-barcodes. BMC Plant Biol 2020; 20:243. [PMID: 32466772 PMCID: PMC7257191 DOI: 10.1186/s12870-020-02435-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 05/10/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Molecular research revealed that some of the European Calypogeia species described on the basis of morphological criteria are genetically heterogeneous and, in fact, are species complexes. DNA barcoding is already commonly used for correct identification of difficult to determine species, to disclose cryptic species, or detecting new taxa. Among liverworts, some DNA fragments, recommend as universal plant DNA barcodes, cause problems in amplification. Super-barcoding based on genomic data, makes new opportunities in a species identification. RESULTS On the basis of 22 individuals, representing 10 Calypogeia species, plastid genome was tested as a super-barcode. It is not effective in 100%, nonetheless its success of species discrimination (95.45%) is still conspicuous. It is not excluded that the above outcome may have been upset by cryptic speciation in C. suecica, as our results indicate. Having the sequences of entire plastomes of European Calypogeia species, we also discovered that the ndhB and ndhH genes and the trnT-trnL spacer identify species in 100%. CONCLUSIONS This study shows that even if a super-barcoding is not effective in 100%, this method does not close the door to a traditional single- or multi-locus barcoding. Moreover, it avoids many complication resulting from the need to amplify selected DNA fragments. It seems that a good solution for species discrimination is a development of so-called "specific barcodes" for a given taxonomic group, based on plastome data.
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Affiliation(s)
- Monika Ślipiko
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Katarzyna Buczkowska
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Alina Bączkiewicz
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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11
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Kulik T, Brankovics B, van Diepeningen AD, Bilska K, Żelechowski M, Myszczyński K, Molcan T, Stakheev A, Stenglein S, Beyer M, Pasquali M, Sawicki J, Wyrȩbek J, Baturo-Cieśniewska A. Diversity of Mobile Genetic Elements in the Mitogenomes of Closely Related Fusarium culmorum and F. graminearum sensu stricto Strains and Its Implication for Diagnostic Purposes. Front Microbiol 2020; 11:1002. [PMID: 32528440 PMCID: PMC7263005 DOI: 10.3389/fmicb.2020.01002] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/24/2020] [Indexed: 12/19/2022] Open
Abstract
Much of the mitogenome variation observed in fungal lineages seems driven by mobile genetic elements (MGEs), which have invaded their genomes throughout evolution. The variation in the distribution and nucleotide diversity of these elements appears to be the main distinction between different fungal taxa, making them promising candidates for diagnostic purposes. Fungi of the genus Fusarium display a high variation in MGE content, from MGE-poor (Fusarium oxysporum and Fusarium fujikuroi species complex) to MGE-rich mitogenomes found in the important cereal pathogens F. culmorum and F. graminearum sensu stricto. In this study, we investigated the MGE variation in these latter two species by mitogenome analysis of geographically diverse strains. In addition, a smaller set of F. cerealis and F. pseudograminearum strains was included for comparison. Forty-seven introns harboring from 0 to 3 endonucleases (HEGs) were identified in the standard set of mitochondrial protein-coding genes. Most of them belonged to the group I intron family and harbored either LAGLIDADG or GIY-YIG HEGs. Among a total of 53 HEGs, 27 were shared by all fungal strains. Most of the optional HEGs were irregularly distributed among fungal strains/species indicating ancestral mosaicism in MGEs. However, among optional MGEs, one exhibited species-specific conservation in F. culmorum. While in F. graminearum s.s. MGE patterns in cox3 and in the intergenic spacer between cox2 and nad4L may facilitate the identification of this species. Thus, our results demonstrate distinctive traits of mitogenomes for diagnostic purposes of Fusaria.
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Affiliation(s)
- Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Balazs Brankovics
- Biointeractions & Plant Health, Wageningen Plant Research, Wageningen, Netherlands
| | | | - Katarzyna Bilska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Maciej Żelechowski
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.,Molecular Biology Laboratory, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Olsztyn, Poland
| | - Tomasz Molcan
- Department of Animal Anatomy and Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Alexander Stakheev
- Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Sebastian Stenglein
- National Scientific and Technical Research Council, Godoy Cruz, Argentina.,Universidad Nacional del Centro de la Provincia de Buenos Aires, Tandil, Argentina
| | - Marco Beyer
- Department of Environmental Research and Innovation, Agro-Environmental Systems, Luxembourg Institute of Science and Technology, Belval, Luxembourg
| | - Matias Pasquali
- Department of Food, Environmental and Nutritional Sciences, University of Milan, Milan, Italy
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Joanna Wyrȩbek
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Anna Baturo-Cieśniewska
- Laboratory of Phytopathology and Molecular Mycology, Department of Biology and Plant Protection, UTP University of Science and Technology, Bydgoszcz, Poland
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12
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Sawicki J, Bączkiewicz A, Buczkowska K, Górski P, Krawczyk K, Mizia P, Myszczyński K, Ślipiko M, Szczecińska M. The Increase of Simple Sequence Repeats during Diversification of Marchantiidae, An Early Land Plant Lineage, Leads to the First Known Expansion of Inverted Repeats in the Evolutionarily-Stable Structure of Liverwort Plastomes. Genes (Basel) 2020; 11:E299. [PMID: 32178248 PMCID: PMC7140840 DOI: 10.3390/genes11030299] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 03/03/2020] [Accepted: 03/10/2020] [Indexed: 01/16/2023] Open
Abstract
The chloroplast genomes of liverworts, an early land plant lineage, exhibit stable structure and gene content, however the known resources are very limited. The newly sequenced plastomes of Conocephalum, Riccia and Sphaerocarpos species revealed an increase of simple sequence repeats during the diversification of complex thalloid liverwort lineage. The presence of long TA motifs forced applying the long-read nanopore sequencing method for proper and dependable plastome assembly, since the length of dinucleotide repeats overcome the length of Illumina short reads. The accumulation of SSRs (simple sequence repeats) enabled the expansion of inverted repeats by the incorporation of rps12 and rps7 genes, which were part of large single copy (LSC) regions in the previously sequenced plastomes. The expansion of inverted repeat (IR) at the genus level is reported for the first time for non-flowering plants. Moreover, comparative analyses with remaining liverwort lineages revealed that the presence of SSR in plastomes is specific for simple thalloid species. Phylogenomic analysis resulted in trees confirming monophyly of Marchantiidae and partially congruent with previous studies, due to dataset-dependent results of Dumortiera-Reboulia relationships. Despite the lower evolutionary rate of Marchantiales plastomes, significant barcoding gap was detected, even for recently divergent holarctic Conocephalum species. The sliding window analyses revealed the presence of 18 optimal (500 bp long) barcodes that enable the molecular identification of all studied species.
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Affiliation(s)
- Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Alina Bączkiewicz
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland; (A.B.); (K.B.)
| | - Katarzyna Buczkowska
- Department of Genetics, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland; (A.B.); (K.B.)
| | - Piotr Górski
- Department of Botany, Poznań University of Life Sciences, 60-625 Poznań, Poland;
| | - Katarzyna Krawczyk
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Patryk Mizia
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
| | - Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn; 10-719 Olsztyn, Poland; (K.K.); (P.M.); (K.M.); (M.Ś.); (M.S.)
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13
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Łopieńska-Biernat E, Paukszto Ł, Jastrzębski JP, Myszczyński K, Polak I, Stryiński R. Genome-wide analysis of Anisakis simplex sensu lato: the role of carbohydrate metabolism genes in the parasite's development. Int J Parasitol 2019; 49:933-943. [PMID: 31560928 DOI: 10.1016/j.ijpara.2019.06.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 06/19/2019] [Accepted: 06/24/2019] [Indexed: 01/08/2023]
Abstract
Anisakis simplex sensu lato is a parasitic nematode which can cause gastric symptoms and/or allergic reactions in humans who consume raw and undercooked fish. Anisakiasis poses a growing health problem around the globe because it causes non-specific symptoms and is difficult to diagnose. This genome-wide study was undertaken to expand our knowledge of A. simplex s.l. at the molecular level and provide novel data for biological and biotechnological research into the analyzed species and related nematodes. A draft genome assembly of the L3 stage of A. simplex s.l. was analyzed in detail, and changes in the expression of carbohydrate metabolism genes during the parasite's life cycle were determined. To our knowledge, this is the first genome to be described for a parasitic nematode of the family Anisakidae to date. We identified genes involved in parasite-specific pathways, including carbohydrates metabolism, apoptosis and chemo signaling. A total of 7607 coding genes were predicted. The genome of A. simplex s.l. is highly similar to genomes of other parasitic nematodes. In particular, we described a valuable repository of genes encoding proteins of trehalose and glycogen metabolism, and we developed the most comprehensive data set relating to the conversion of both saccharides which play important roles during the parasite's life cycle in a host environment. We also confirmed that trehalose is synthesized at the expense of glycogen. Trehalose anabolism and glycogen catabolism were the predominant processes in stages L4 and L5, which could confirm our and other authors' previous reports that trehalose is synthesized at the expense of glycogen. The A. simplex s.l. genome provides essential data for post-genomic research into the biology of gastrointestinal and allergic anisakiasis in humans and the biology of other important parasitic helminths.
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Affiliation(s)
- Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland
| | - Iwona Polak
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Robert Stryiński
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
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14
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Myszczyński K, Ślipiko M, Sawicki J. Potential of Transcript Editing Across Mitogenomes of Early Land Plants Shows Novel and Familiar Trends. Int J Mol Sci 2019; 20:E2963. [PMID: 31216623 PMCID: PMC6627324 DOI: 10.3390/ijms20122963] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2019] [Revised: 06/15/2019] [Accepted: 06/17/2019] [Indexed: 01/04/2023] Open
Abstract
RNA editing alters the identity of nucleotides in an RNA sequence so that the mature transcript differs from the template defined in the genome. This process has been observed in chloroplasts and mitochondria of both seed and early land plants. However, the frequency of RNA editing in plant mitochondria ranges from zero to thousands of editing sites. To date, analyses of RNA editing in mitochondria of early land plants have been conducted on a small number of genes or mitochondrial genomes of a single species. This study provides an overview of the mitogenomic RNA editing potential of the main lineages of these two groups of early land plants by predicting the RNA editing sites of 33 mitochondrial genes of 37 species of liverworts and mosses. For the purpose of the research, we newly assembled seven mitochondrial genomes of liverworts. The total number of liverwort genera with known complete mitogenome sequences has doubled and, as a result, the available complete mitogenome sequences now span almost all orders of liverworts. The RNA editing site predictions revealed that C-to-U RNA editing in liverworts and mosses is group-specific. This is especially evident in the case of liverwort lineages. The average level of C-to-U RNA editing appears to be over three times higher in liverworts than in mosses, while the C-to-U editing frequency of the majority of genes seems to be consistent for each gene across bryophytes.
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Affiliation(s)
- Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn, Plac Łódzki 1, 10-727 Olsztyn, Poland.
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15
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Myszczyński K, Górski P, Ślipiko M, Sawicki J. Sequencing of organellar genomes of Gymnomitrion concinnatum (Jungermanniales) revealed the first exception in the structure and gene order of evolutionary stable liverworts mitogenomes. BMC Plant Biol 2018; 18:321. [PMID: 30509184 PMCID: PMC6276189 DOI: 10.1186/s12870-018-1558-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/22/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND Comparative analyses of chloroplast and mitochondrial genomes have shown that organelle genomes in bryophytes evolve slowly. However, in contrast to seed plants, the organellar genomes are yet poorly explored in bryophytes, especially among liverworts. Discovering another organellar genomes of liverwort species by sequencing provides new conclusions on evolution of bryophytes. RESULTS In this work, the organellar genomes of Gymnomitrion concinnatum liverwort were sequenced, assembled and annotated for the first time. The chloroplast genome displays, typical for most plants, quadripartite structure containing large single copy region (81,701 bp), two inverted repeat regions (8704 bp each) and small single copy region (20,179 bp). The gene order and content of chloroplast are very similar to other liverworts with minor differences observed. A total number of 739 and 222 RNA editing sites were predicted in chloroplast and mitochondrial genes of G. concinnatum. The mitochondrial genome gene content is also in accordance with liverworts except few alterations such as: intron loss in cox1 and atp1 genes. Nonetheless the analysis revealed that G. concinnatum mitogenome structure and gene order are rearranged in comparison with other mitogenomes of liverworts. The causes underlying such mitogenomic rearrangement were investigated and the probable model of recombination was proposed. CONCLUSIONS This study provide the overview of mitochondrial and chloroplast genome structure and gene order diversity of Gymnomitrion concinnatum against the background of known organellar genomes of liverworts. The obtained results cast doubt on the idea that mitogenome structure of early land plants is highly conserved as previous studies suggested. In fact is the very first case of recombination within, evolutionary stable, mitogenomes of liverworts.
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Affiliation(s)
- Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Piotr Górski
- Department of Botany, Poznań University of Life Sciences, Poznań, Poland
| | - Monika Ślipiko
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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16
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Krawczyk K, Nobis M, Myszczyński K, Klichowska E, Sawicki J. Plastid super-barcodes as a tool for species discrimination in feather grasses (Poaceae: Stipa). Sci Rep 2018; 8:1924. [PMID: 29386579 PMCID: PMC5792575 DOI: 10.1038/s41598-018-20399-w] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2017] [Accepted: 01/17/2018] [Indexed: 02/03/2023] Open
Abstract
Present study was designed to verify which or if any of plastome loci is a hotspot region for mutations and hence might be useful for molecular species identification in feather grasses. 21 newly sequenced complete plastid genomes representing 19 taxa from the genus of Stipa were analyzed in search of the most variable and the most discriminative loci within Stipa. The results showed that the problem with selecting a good barcode locus for feather grasses lies in the very low level of genetic diversity within its plastome. None of the single chloroplast loci is polymorphic enough to play a role of a barcode or a phylogenetic marker for Stipa. The biggest number of taxa was successfully identified by the analysis of 600 bp long DNA fragment comprising a part of rbcL gene, the complete rbcL-rpl23 spacer and a part of rpl23 gene. The effectiveness of multi-locus barcode composed of six best-performing loci for Stipa (ndhH, rpl23, ndhF-rpl32, rpl32-ccsA, psbK-psbI and petA-psbJ) didn't reach 70% of analyzed taxa. The analysis of complete plastome sequences as a super-barcode for Stipa although much more effective, still didn't allow for discrimination of all the analyzed taxa of feather grasses.
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Affiliation(s)
- Katarzyna Krawczyk
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland.
| | - Marcin Nobis
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
| | - Ewelina Klichowska
- Institute of Botany, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Olsztyn, Poland
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17
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Łopieńska-Biernat E, Molcan T, Paukszto Ł, Jastrzębski JP, Myszczyński K. Modelling studies determing the mode of action of anthelmintics inhibiting in vitro trehalose-6-phosphate phosphatase (TPP) of Anisakis simplex s.l. Exp Parasitol 2017; 184:46-56. [PMID: 29170085 DOI: 10.1016/j.exppara.2017.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 10/20/2017] [Accepted: 11/17/2017] [Indexed: 10/18/2022]
Abstract
The trehalose-6-phosphate phosphatase (TPP) enzyme is involved in the synthesis of trehalose, the main sugar in the energy metabolism of nematodes. TPP is a member of the HAD-like hydrolase superfamily and shows a robust and specific phosphatase activity for the substrate trehalose-6-phosphate. The presence of conserved active sites of TPP in closely related nematodes and its absence in humans makes it a promising target for antiparasitic drugs. In the present study, homology modeling, molecular docking and MD simulation techniques were used to explore the structure and dynamics of TPP. In the active site, a magnesium ion is stabilized by 3 coordinate bonds formed by D189, D191 and D400. The key amino acids involved in ligand binding by the enzyme are C198, Y201,T357, D191 and Y197. This study relied on docking to select potential inhibitors of TPP which were tested in vitro for sensitivity to anthelmintic drugs such as levamisole and ivermectin targeting Anisakis simplex. The higher toxicity of LEV than IVM was demonstrated after 96 h, 30% of larvae were motile in cultures with 100 μg/ml of LEV and 1000 μg/ml of IVM. We identified drug combination of LEV-IVM against in vitro A. simplex as agonistic effect (CI = 1.1). Levamisole appeared to be a more effective drug which inhibited enzyme activity after 48 h and expression of mRNA after 96 h at a concentration of 10 μg/ml. This preliminary study predicted the structure of TPP, and the results of an in vitro experiment involving A. simplex will contribute to the development of effective inhibitors with potential antiparasitic activity in the future.
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Affiliation(s)
- Elżbieta Łopieńska-Biernat
- Department of Biochemistry, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland.
| | - Tomasz Molcan
- Department of Animal Physiology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Jan Paweł Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University Warmia and Mazury in Olsztyn, Oczapowskiego 1A, 10-719 Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, Poland
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Myszczyński K, Bączkiewicz A, Buczkowska K, Ślipiko M, Szczecińska M, Sawicki J. The extraordinary variation of the organellar genomes of the Aneura pinguis revealed advanced cryptic speciation of the early land plants. Sci Rep 2017; 7:9804. [PMID: 28852146 PMCID: PMC5575236 DOI: 10.1038/s41598-017-10434-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 08/09/2017] [Indexed: 11/09/2022] Open
Abstract
Aneura pinguis is known as a species complex with several morphologically indiscernible species, which are often reproductively isolated from each other and show distinguishable genetic differences. Genetic dissimilarity of cryptic species may be detected by genomes comparison. This study presents the first complete sequences of chloroplast and mitochondrial genomes of six cryptic species of A. pinguis complex: A. pinguis A, B, C, E, F, J. These genomes have been compared to each other in order to reconstruct phylogenetic relationships and to gain better understanding of the evolutionary process of cryptic speciation in this complex. The chloroplast genome with the nucleotide diversity 0.05111 and 1537 indels is by far more variable than mitogenome with π value 0.00233 and number of indels 1526. Tests of selection evidenced that on about 36% of chloroplast genes and on 10% of mitochondrial genes of A. pinguis acts positive selection. It suggests an advanced speciation of species. The phylogenetic analyses based on genomes show that A. pinguis is differentiated and forms three distinct clades. Moreover, on the cpDNA trees, Aneura mirabilis is nested among the cryptic species of A. pinguis. This indicates that the A. pinguis cryptic species do not derive directly from one common ancestor.
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Affiliation(s)
- Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland.
| | - Alina Bączkiewicz
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Katarzyna Buczkowska
- Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
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Krawczyk K, Wiland-Szymańska J, Buczkowska-Chmielewska K, Drapikowska M, Maślak M, Myszczyński K, Szczecińska M, Ślipiko M, Sawicki J. The complete chloroplast genome of a rare orchid species Liparis loeselii (L.). CONSERV GENET RESOUR 2017. [DOI: 10.1007/s12686-017-0809-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Sawicki J, Plášek V, Ochyra R, Szczecińska M, Ślipiko M, Myszczyński K, Kulik T. Mitogenomic analyses support the recent division of the genus Orthotrichum (Orthotrichaceae, Bryophyta). Sci Rep 2017; 7:4408. [PMID: 28667304 PMCID: PMC5493672 DOI: 10.1038/s41598-017-04833-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/22/2017] [Indexed: 11/22/2022] Open
Abstract
A recently presented taxonomical arrangement of the moss genus Orthotrichum Hedw. s.l. substantially changed the traditional view of the taxon that had been accepted throughout the twentieth century. This paper provides the results of mitogenomic studies that strongly support the new taxonomical concept. Comparative analyses presented in this study confirmed the stable structure of moss mitogenomes. Moreover, 17 complete mitogenome sequences were used to identify the major evolutionary groups, including 11 newly sequenced ones, for this study. The analysis of mitochondrial hotspots revealed intron 4 of the cox1 gene to be the most variable non-coding region. The most variable protein-coding genes in the tribe Orthotricheae were ccmFC and tatC. The intergenic and intronic hotspots of Orthotrichum s.l. identified in the present study do not correspond to those described in vascular plant mitogenomes.
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Affiliation(s)
- Jakub Sawicki
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland.
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic.
| | - Vítězslav Plášek
- Department of Biology and Ecology, University of Ostrava, Chittussiho 10, 710 00, Ostrava, Czech Republic
| | - Ryszard Ochyra
- Laboratory of Bryology, Institute of Botany, Polish Academy of Sciences, Lubicz 46, 31-512, Kraków, Poland
| | - Monika Szczecińska
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Monika Ślipiko
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Kamil Myszczyński
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
| | - Tomasz Kulik
- Department of Botany and Nature Protection, University of Warmia and Mazury, Plac Łódzki 1, 10-727, Olsztyn, Poland
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Myszczyński K, Bączkiewicz A, Szczecińska M, Buczkowska K, Kulik T, Sawicki J. The complete mitochondrial genome of the cryptic species C of Aneura pinguis. Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:112-113. [PMID: 26678523 DOI: 10.3109/19401736.2015.1111347] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The structure of the Aneura pinguis mitochondrial genome (GenBank accession no. NC_026901) is similar to that of closely related Metzgeriales species: it has a total length of 165 603 bp, the base composition of the mitogenome is the following: A (26.2%), C(23.6%), G(23.8%), and T(26.4%). The A. piguis mitochondrial genome contains 69 genes. A complete mitochondrial genome sequence of A. pinguis will help better to understand mitogenome structure and content among Metzgeriales order.
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Affiliation(s)
- Kamil Myszczyński
- a Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Alina Bączkiewicz
- b Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań , Poznań , Poland , and
| | - Monika Szczecińska
- a Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Katarzyna Buczkowska
- b Department of Biology, Institute of Experimental Biology, Adam Mickiewicz University in Poznań , Poznań , Poland , and
| | - Tomasz Kulik
- a Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Jakub Sawicki
- a Department of Botany and Nature Protection, University of Warmia and Mazury in Olsztyn , Olsztyn , Poland.,c Department of Biology and Ecology, University of Ostrava , Ostrava , Czech Republic
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Myszczyński K, Nobis M, Szczecinska M, Sawicki J, Nowak A. The complete plastid genome of the middle Asian endemic of Stipa lipskyi (Poaceae). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:4661-4662. [PMID: 26678247 DOI: 10.3109/19401736.2015.1106491] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The structure of the Stipa lipskyi (GenBank accession no. KT692644) plastid genome is similar to that of closely related Poaceae species: it has a total length of 137 755 bp, the base composition of the plastome is the following: A (30.7%), C (19.3%), G (19.4%) and T (30.5%). The S. lipskyi plastid genome contains 71 genes, excluding second IR region. A complete plastome sequence of S. lipskyi will help the development of primers for examining phylogeny and hybridization events in this taxonomically difficult genus.
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Affiliation(s)
- Kamil Myszczyński
- a Department of Botany and Nature Protection , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Marcin Nobis
- b Department of Plant Taxonomy , Phytogeography & Herbarium, Institute of Botany, Jagiellonian University , Kraków , Poland
| | - Monika Szczecinska
- a Department of Botany and Nature Protection , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland
| | - Jakub Sawicki
- a Department of Botany and Nature Protection , University of Warmia and Mazury in Olsztyn , Olsztyn , Poland.,c Department of Biology and Ecology , University of Ostrava , Ostrava , Czech Republic , and
| | - Arkadiusz Nowak
- c Department of Biology and Ecology , University of Ostrava , Ostrava , Czech Republic , and.,d Laboratory of Geobotany and Plant Conservation, Department of Biosystematics , Opole University , Opole , Poland
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Jakub S, Szczecińska M, Kulik T, Myszczyński K, Ślipiko M, Wołosz K, Plášek V. The complete mitochondrial genome of the rare and endangered Orthotrichum rogeri (Orthotrichaceae, Bryophyta). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 27:3208-9. [PMID: 25758046 DOI: 10.3109/19401736.2015.1007349] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The mitogenome of the Orthotrichum rogeri (GenBank accession number KM873610) has a total length of 106,634 bp and consist of 40 protein-coding genes, 3 ribosomal RNA (rRNA) and 24 transfer RNA. The gene order is identical to other known moss mitogenomes. A complete mitochondrial genome sequence of O. rogeri will help the development of primers for examining mitochondrial variation across bryophytes.
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Affiliation(s)
- Sawicki Jakub
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and.,b Department of Biology and Ecology , University of Ostrava , Ostrava , Czech Republic
| | - Monika Szczecińska
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and
| | - Tomasz Kulik
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and
| | - Kamil Myszczyński
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and
| | - Monika Ślipiko
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and
| | - Katarzyna Wołosz
- a Department of Botany and Nature Protection , University of Warmia and Mazury , Olsztyn , Poland and
| | - Vítězslav Plášek
- b Department of Biology and Ecology , University of Ostrava , Ostrava , Czech Republic
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