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Palacıoğlu G, Alkan M, Derviş S, Bayraktar H, Özer G. Molecular phylogeny of plant pathogenic fungi based on start codon targeted (SCoT) polymorphism. Mol Biol Rep 2023; 50:8271-8279. [PMID: 37578578 DOI: 10.1007/s11033-023-08735-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 08/02/2023] [Indexed: 08/15/2023]
Abstract
BACKGROUND A number of molecular marker systems have been developed to assess genetic diversity, carry out phylogenetic analysis, and diagnose and discriminate plant pathogenic fungi. The start codon targeted (SCoT) markers system is a novel approach used here to investigate intra and interspecific polymorphisms of phytopathogenic fungi. MATERIALS AND METHODS This study assessed genetic variability between and within 96 isolates of ten fungal species associated with a variety of plant species using 36 SCoT primers. RESULTS The six primers generated 331 distinct and reproducible banding patterns, of which 322 were polymorphic (97.28%), resulting in 53.67 polymorphic bands per primer. All primers produced informative amplification profiles that distinguished all fungal species. With a resolving power of 10.65, SCoT primer 12 showed the highest polymorphism among species, followed by primer 33 and primer 29. Polymorphic loci (PPL), Nei's diversity index (h), and Shannon index (I) percentages were 6.25, 0.018, and 0.028, respectively. UPGMA analysis separated all isolates based on morphological classification and revealed significant genetic variation among fungal isolates at the intraspecific level. PCoA analysis strongly supported fungal species discrimination and genetic variation. The other parameters of evaluation proved that SCoT markers are at least as effective as other DNA markers. CONCLUSIONS SCoT markers were effective in identifying plant pathogenic fungi and were a powerful tool for estimating genetic variation and population structure of different fungi species.
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Affiliation(s)
- Gülsüm Palacıoğlu
- Department of Plant Protection, Faculty of Agriculture, Şırnak University, Şırnak, Turkey
| | - Mehtap Alkan
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Sibel Derviş
- Department of Plant and Animal Production, Vocational School of Kızıltepe, Mardin Artuklu University, Mardin, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey.
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
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Liu JH, Ding FH, Song HY, Chen MH, Hu DM. Analysis of genetic diversity among Chinese Cyclocybe chaxingu strains using ISSR and SRAP markers. PeerJ 2022; 10:e14037. [PMID: 36196401 PMCID: PMC9527026 DOI: 10.7717/peerj.14037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/18/2022] [Indexed: 01/19/2023] Open
Abstract
Background Cyclocybe chaxingu is an edible and medicinal fungal species commonly cultivated in China. The major problems currently facing by growers of C. chaxingu is the random labeling of strains and strains aging and degeneration. Therefore, an evaluation of genetic diversity is essential for the conservation and reproducing programs of this species. Methods In the present study, 24 widely cultivated strains were collected from the main producing areas of China, and the genetic diversity analysis was performed. DNA polymorphism among these Chinese C. chaxingu strains was analyzed using inter-simple sequence repeat (ISSR) and sequence-related amplified polymorphism (SRAP) markers. Results Eight ISSR primers amplified a total of 75 DNA fragments of which 61 (81.33%) were polymorphic. Fifteen SRAP primer combinations amplified 166 fragments of which 132 (79.52%) were polymorphic. Cluster analysis showed that the C. chaxnigu strains fall into five groups with a genetic distance values ranging from 0.06 to 0.60 by ISSR analysis, while the SRAP analysis divided the test strains into four groups within the range of genetic distance from 0.03 to 0.57. The results of the present study reveal a high level of genetic diversity among the widely cultivated C. chaxingu strains.
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Affiliation(s)
- Jin-Hao Liu
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
| | - Fang-Hui Ding
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China
| | - Hai-Yan Song
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Ministry of Education of the P.R. China, Key Laboratory of Crop Physiology, Ecology and Genetic Breeding (Jiangxi Agricultural University), Nanchang, China
| | - Ming-Hui Chen
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
| | - Dian-Ming Hu
- Jiangxi Agricultural University, Bioengineering and Technological Research Centre for Edible and Medicinal Fungi, Nanchang, China,Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, China,Jiangxi Key Laboratory for Conservation and Utilization of Fungal Resources, and College of Bioscience and Bioengineering, Nanchang, China
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Virulence Structure and Genetic Diversity of Blumeria graminis f. sp. avenae from Different Regions of Europe. PLANTS 2022; 11:plants11101358. [PMID: 35631783 PMCID: PMC9145444 DOI: 10.3390/plants11101358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 05/14/2022] [Accepted: 05/18/2022] [Indexed: 11/17/2022]
Abstract
The structure and dynamics of changes in pathogen populations can be analysed by assessing the level of virulence and genetic diversity. The aim of the present study was to determine the diversity of Blumeria graminis f. sp. avenae populations. Diversity and virulence of B. graminis f. sp. avenae was assessed based on 80 single-spore isolates collected in different European countries such as Poland (40 isolates), Germany (10), Finland (10), Czech Republic (10) and Ireland (10) using ISSR (Inter-Simple Sequence Repeats) and SCoT (Start Codon Targeted) markers. This work demonstrated differences in virulence of B. graminis f. sp. avenae isolates sampled from different countries. Molecular analysis showed that both systems were useful for assessing genetic diversity, but ISSR markers were superior and generated more polymorphic products, as well as higher PIC and RP values. UPMGA and PCoA divided the isolates into groups corresponding with their geographical origin. In conclusion, the low level of genetic differentiation of the analysed isolates has suggested that the evolution of B. graminis f. sp. Avenae population is slow, and thus the evolutionary potential of the pathogen is low. This work paves the way for future studies on B. graminis f. sp. Avenae population structure and dynamics based on genetic variability.
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Salim RG, Fadel M, Youssef YA, Taie HAA, Abosereh NA, El-Sayed GM, Marzouk M. A local Talaromyces atroroseus TRP-NRC isolate: isolation, genetic improvement, and biotechnological approach combined with LC/HRESI-MS characterization, skin safety, and wool fabric dyeing ability of the produced red pigment mixture. J Genet Eng Biotechnol 2022; 20:62. [PMID: 35451646 PMCID: PMC9033925 DOI: 10.1186/s43141-022-00335-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 02/18/2022] [Indexed: 11/12/2022]
Abstract
Background During the last decade, enormous research efforts have been directed at identifying potent microorganisms as sustainable green cell factories for eco-friendly pigments. Talaromyces atroroseus has recently been shown to excrete large amounts of azaphilone mycotoxin-free red pigment mixture comprising some known coloring components together with many uncharacterized metabolites. In this study, a new Talaromyces atroroseus isolate was identified via sequencing of the fragment of the nuclear ribosomal gene cluster containing internal transcribed spacers and 5.8S rRNA gene. The parameters that affected the level of pigment production were optimized in uncommon static conditions of culture and genetic improvement, via γ-irradiation, to improve pigment yield. Moreover, chemical characterization using LC/MS and skin safety test of the target pigment mixture were precisely conducted to maximize its benefits as a natural and safe red pigment for wool fabrics. Results Molecular identification via the sequencing of the ITS of the rDNA encoding gene cluster revealed that the fungal isolate TRP-NRC was T. atroroseus TRP-NRC (deposited in GenBank under accession number MW282329). In the static conditions of culture, pigment production was dramatically enhanced to 27.36 g/L in an optimum yeast malt peptone medium of 2% mannitol at pH 2−4.5 and 30 °C for 7 days of incubation. Under exposure to a 400-Gy γ-radiation dose, pigment yield was increased to a 3-fold level higher than that recorded for the wild type. Based on the inter-simple sequence repeats (ISSR), as a molecular marker tool, the wild-type T. atroroseus TRP-NRC strain and its mutants were discriminated. The UHPLC/HRESI-MS analytical tool characterized 60 metabolites, including many unknown molecules, at appropriate concentrations. It is worthy to note that four mitorubrin derivatives were identified for the first time in T. atroroseus, i.e., mitorubrinolamine acetate, dihydro-PP-O, mitorobrinal, and mitorubrinol. The range of irritation indexes (0−0.1) demonstrated an adequate skin safety after the direct local application of the pigment mixture. Finally, the pigment mixture exhibited a remarkably good dyeing ability in wool fabrics, with high-fastness properties. Conclusions Because of its sustainable and economic production, the target red pigment mixture may be applied in the future in textile, food, cosmetics, or different pharmaceutical industries after extensive conventional safety and toxicity studies, which are currently under consideration. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00335-2.
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Affiliation(s)
- Rasha G Salim
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Mohamed Fadel
- Microbial Chemistry Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Yehya A Youssef
- Department of Dyeing, Printing and Auxiliaries, Textile Technology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Hanan A A Taie
- Plant Biochemistry Department, Agricultural and Biology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Nivien A Abosereh
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Ghada M El-Sayed
- Microbial Genetic Department, Biotechnology Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt
| | - Mohamed Marzouk
- Chemistry of Tanning Materials and Leather Technology Department, Chemical Industries Research Institute, National Research Centre, 33 El-Bohouth St. (Former El-Tahrir St.), Dokki, Cairo, 12622, Egypt.
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Characterization of Mutant Aspergillus niger and the Impact on Certain Plants. SUSTAINABILITY 2022. [DOI: 10.3390/su14031936] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Aspergillus niger is a dangerous pathogen for many plants. It is a major cause of the destruction, rotting and decomposition of plant tissues. Toxicity caused by A. niger can be inhibited by mutation decreasing the destructive effect on plants. An 18S rDNA molecular tool was used to identify A. niger strains. Sodium azide (NaN3) is a chemical mutagen that disturbs fungal enzymatic activity and causes microbial production of cellulose-degrading enzymes, decreasing mycotoxin production. Different concentrations of sodium azide were used to treat A. niger (30, 40 and 50 µM). The study was designed on two levels: the first level concerned the mutant A. niger’s mode of action: the higher the mutagen concentration, the lower the growth diameter and spore counts. The mutant A. niger’s total proteins and flavonoids were reduced when compared to control. RAPD-PCR showed genetic variation in the genetic content of mutant fungi compared to control resulting in a polymorphism percentage of 78.56%. The second level included the effect of these mutants on two plants (onion and maize). The greater the increase in mutant concentration, the greater the increase in the plants’ morphological and physiological behavior. In conclusion, mutation reduced fungal activity and strengthened plant resistance.
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Zelmat L, Mansi JM, Aouzal S, Gaboun F, Khayi S, Ibriz M, El Guilli M, Mentag R. Genetic Diversity and Population Structure of Moroccan Isolates Belong to Alternaria spp. Causing Black Rot and Brown Spot in Citrus. Int J Genomics 2021; 2021:9976969. [PMID: 34859097 PMCID: PMC8632404 DOI: 10.1155/2021/9976969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 09/21/2021] [Accepted: 10/12/2021] [Indexed: 11/23/2022] Open
Abstract
Alternaria alternata is one of the most important fungi causing various diseases on citrus worldwide. In Morocco, Alternaria black rot (ABR) and Alternaria brown spot (ABS) are two major diseases causing serious losses in commercial cultivars of citrus. The aim of the present work was to study the genetic diversity and the population structure of isolates belonging to sect. Alternaria obtained from infected citrus fruits, collected from seven provinces at different locations in Morocco (markets, packinghouses, and orchards). Forty-five isolates were analyzed by sequence-related amplified polymorphism (SRAP) markers, and cluster analysis of DNA fragments was performed using UPGMA method and Jaccard coefficient. Cluster analysis revealed that isolates were classified in four distinct groups. AMOVA revealed also a large extent of variation within sect. Alternaria isolates (99%). The results demonstrate that no correlation was found among SRAP pattern, host, and geographical origin of these isolates. Population structure analyses showed that the Alternaria isolates from the same collection origin had almost a similar level of admixture.
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Affiliation(s)
- Lamyaa Zelmat
- Plant Pathology and Postharvest Quality laboratory, Plant Protection Research Unit, Regional Center of Agricultural Research of Kénitra, National Institue of Agricultural Research, El Menzeh Km 9, 14000, Kénitra, Morocco
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Department of Biology, Genetics and Biometrics Laboratory, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Joseph Mbasani Mansi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Department of Biology, Higher Institute of Medical Techniques (ISTM) Kinshasa, Democratic Republic of the Congo
| | - Sarra Aouzal
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
- Agro-Food and Health Laboratory, Faculty of Science and Techniques, Hassan First University of Settat, Settat, Morocco
| | - Fatima Gaboun
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Slimane Khayi
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
| | - Mohammed Ibriz
- Department of Biology, Genetics and Biometrics Laboratory, Faculty of Sciences, Ibn Tofail University, Kénitra, Morocco
| | - Mohammed El Guilli
- Plant Pathology and Postharvest Quality laboratory, Plant Protection Research Unit, Regional Center of Agricultural Research of Kénitra, National Institue of Agricultural Research, El Menzeh Km 9, 14000, Kénitra, Morocco
| | - Rachid Mentag
- Biotechnology Research Unit, Regional Center of Agricultural Research of Rabat, National Institute of Agricultural Research, Avenue Ennasr, BP 415 Rabat Principale, 10090, Rabat, Morocco
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Adhikari S, Joshi SM, Athoni BK, Patil PV, Jogaiah S. Elucidation of genetic relatedness of Magnaporthe grisea, an incitent of pearl millet blast disease by molecular markers associated with virulence of host differential cultivars. Microb Pathog 2020; 149:104533. [PMID: 32980470 DOI: 10.1016/j.micpath.2020.104533] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/23/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Abstract
In recent years, blast disease caused by Magnaporthe grisea, an ascomycete fungus is becoming a serious threat to pearl millet crop in India and worldwide. Due to the increase in virulent races of pathogen, blast disease management strategies seemed to be very limited. Hence, unraveling the occurrence of blast isolates across India and understanding their virulence and genetic relatedness using molecular markers are the key objectives of this study. From Farmer's field survey we have evidenced variability in blast pathogen across India by recording 10.6 to 7.9 disease severities. A fair to good variation in cultural and conidial characters were also noticed for 17 field isolates. The identity of 17 isolates was confirmed as Magnaporthe grisea by internal transcribed spacer (ITS) region. Based on 12 host differential virulence reactions, five isolates BgKMg1, BdmMg2, MtgMg11, JprMg16 and JmnMg17 recorded highly susceptible (>5 grade) to nine differentials used in the study. While, host differentials ICMB95444, ICMR06222, ICMR11003, IP21187 and ICMV155 found effective for screening virulence of blast disease. Furthermore, genetic relatedness assessed by ITS, inter simple sequence repeats (ISSR) and simple sequence repeats (SSR) markers produced high degree of polymorphism and was able to distinguish the virulence pattern of 17 isolates that correlated with phenotypic screening. Among markers, clustering of isolates within groups was significantly different with remarkable genetic similarity coefficient and bootstrap values. Overall, these results confirm a significant morphological and genetic variation among 17 isolates, thereby helping to elucidate the virulence of pearl millet blast populations in India that could avoid breakdown of resistance and assist breeding improved pearl millet cultivars.
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Affiliation(s)
- Shivakantkumar Adhikari
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad, 580 003, Karnataka, India
| | - Shreya M Joshi
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad, 580 003, Karnataka, India
| | - Bandenamaj K Athoni
- AICRP-Pearl Millet, Regional Agricultural Research Station (RARS), Hittnalli Farm, Vijayapur, 586101, Karnataka, India
| | - Prakashgouda V Patil
- Department of Plant Pathology, University of Agricultural Sciences, Dharwad, 580 005, Karnataka, India
| | - Sudisha Jogaiah
- Laboratory of Plant Healthcare and Diagnostics, PG Department of Studies in Biotechnology and Microbiology, Karnatak University, Pavate Nagar, Dharwad, 580 003, Karnataka, India.
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