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Jiménez-Gaona Y, Vivanco-Galván O, Cruz D, Armijos-Carrión A, Suárez JP. Compensatory Base Changes in ITS2 Secondary Structure Alignment, Modelling, and Molecular Phylogeny: An Integrated Approach to Improve Species Delimitation in Tulasnella (Basidiomycota). J Fungi (Basel) 2023; 9:894. [PMID: 37755002 PMCID: PMC10532482 DOI: 10.3390/jof9090894] [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] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/08/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND The delimitation of species of Tulasnella has been extensively studied, mainly at the morphological (sexual and asexual states) and molecular levels-showing ambiguity between them. An integrative species concept that includes characteristics such as molecular, ecology, morphology, and other information is crucial for species delimitation in complex groups such as Tulasnella. OBJECTIVES The aim of this study is to test evolutionary relationships using a combination of alignment-based and alignment-free distance matrices as an alternative molecular tool to traditional methods, and to consider the secondary structures and CBCs from ITS2 (internal transcribed spacer) sequences for species delimitation in Tulasnella. METHODOLOGY Three phylogenetic approaches were plotted: (i) alignment-based, (ii) alignment-free, and (iii) a combination of both distance matrices using the DISTATIS and pvclust libraries from an R package. Finally, the secondary structure consensus was modeled by Mfold, and a CBC analysis was obtained to complement the species delimitation using 4Sale. RESULTS AND CONCLUSIONS The phylogenetic tree results showed delimited monophyletic clades in Tulasnella spp., where all 142 Tulasnella sequences were divided into two main clades A and B and assigned to seven species (T. asymmetrica, T. andina, T. eichleriana ECU6, T. eichleriana ECU4 T. pinicola, T. violea), supported by bootstrap values from 72% to 100%. From the 2D secondary structure alignment, three types of consensus models with helices and loops were obtained. Thus, T. albida belongs to type I; T. eichleriana, T. tomaculum, and T. violea belong to type II; and T. asymmetrica, T. andina, T. pinicola, and T. spp. (GER) belong to type III; each type contains four to six domains, with nine CBCs among these that corroborate different species.
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Affiliation(s)
- Yuliana Jiménez-Gaona
- Departamento de Química, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador
| | - Oscar Vivanco-Galván
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Darío Cruz
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
| | - Angelo Armijos-Carrión
- Department of Biology, Memorial University of Newfoundland, St. John’s, NL A1B 3X9, Canada;
| | - Juan Pablo Suárez
- Departamento de Ciencias Biológicas, Universidad Técnica Particular de Loja (UTPL), San Cayetano Alto s/n, Loja 1101608, Ecuador; (O.V.-G.); (D.C.); (J.P.S.)
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Hasan AEZ, Julistiono H, Bermawie N, Riyanti EI, Arifni FR. Soursop leaves (Annona muricata L.) endophytic fungi anticancer activity against HeLa cells. Saudi J Biol Sci 2022; 29:103354. [PMID: 35813114 PMCID: PMC9256652 DOI: 10.1016/j.sjbs.2022.103354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 05/11/2022] [Accepted: 06/15/2022] [Indexed: 12/24/2022] Open
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Coats K, Debauw A, Lakshman DK, Roberts DP, Ismaiel A, Chastagner G. Detection and Molecular Phylogenetic-Morphometric Characterization of Rhizoctonia tuliparum, Causal Agent of Gray Bulb Rot of Tulips and Bulbous Iris. J Fungi (Basel) 2022; 8:163. [PMID: 35205917 PMCID: PMC8880388 DOI: 10.3390/jof8020163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 01/31/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
Gray bulb rot of tulips and bulbous iris is caused by the soil-borne fungal pathogen, Rhizoctonia tuliparum (Rtul). Sclerotia present in infected bulbs, as well as overwintering sclerotia in soil and field debris, are the primary sources of infection. A method for accurate and sensitive detection of Rtul from soil and infected bulbs, and estimation of inoculum threshold levels, is needed for the management of disease caused by this pathogen. We designed a unique set of primers targeting the ITS2 region of the Rtul genome and developed a highly sensitive quantitative PCR (qPCR)-based method for Rtul identification using these primers, where the threshold of detection was approximately 1 fg Rtul DNA. The assay was more sensitive with sclerotia collected from the field (natural) than with those grown in the lab, and more sensitive with natural-light than natural-dark sclerotia. Also, the detection method was more sensitive when sclerotia were extracted from soil than from bulb tissue. The qPCR method was highly specific, as no PCR amplification was detected when genomic DNA from 62 non-Rtul Rhizoctonia isolates from a wide range of anastomosis groups were tested. To understand the evolutionary relationships and genomic diversity of Rtul, we performed phylogenetics of the ITS1-5.8S-ITS2 region and ITS2-molecular morphometric characterization (MMC) of Rtul isolates. The three Rtul isolates whose ITS sequences were available in GenBank formed a distinct phylogenetic clade with Ceratobasidium anceps as the nearest relative. Furthermore, MMC analysis revealed genetic divergence among these three Rtul isolates.
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Singh V, Lakshman DK, Roberts DP, Ismaiel A, Hooda KS, Gogoi R. Morphopathological and Molecular Morphometric Characterization of Waitea circinata var. prodigus Causing a Novel Sheath Spot Disease of Maize in India. Plant Dis 2022; 106:526-534. [PMID: 34261356 DOI: 10.1094/pdis-05-21-0951-re] [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] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Maize brown sheath spot (MBSS), a new disease of maize, was discovered while surveying for maize leaf and sheath blight diseases in the Indian states of Assam, Jharkhand, Meghalaya, Manipur, and Odisha. Maize is the third most important cereal after rice and wheat in India. Unlike banded leaf and sheath blight disease caused by Rhizoctonia solani, MBSS symptoms on maize were discrete and limited to sheaths only. Symptoms of MBSS in the field were initially water-soaked necrotic lesions of 1 to 2 cm in diameter on the lowermost leaf sheaths, which then progressed to the upper sheaths. Lesions coalesced and covered approximately 2 to 5% of the sheath area. Infected dried lower leaves were shed, whereas infected upper leaves remained on the stem. The pathogen was isolated, characterized morphologically, pathologically, and molecularly, and identified as Waitea circinata var. prodigus, a basidiomycete known to cause basal leaf blight of seashore paspalum. The internal transcribed spacer (ITS) sequence 2 (ITS2) of rDNA from MBSS isolates formed a well supported clade with known W. circinata var. prodigus isolates. Molecular morphometric analysis of the ITS2 regions of the five known varieties of W. circinata detected distinguishing variations in GC content, compensatory base changes (CBCs), hemi- CBCs, indels, and altered base-pairing of helices. Variation in these characteristics may indicate that varieties are distinct biological species within W. circinata sensu lato. The geographical distribution and potential impacts of MBSS on the maize crop in India necessitate further investigations of pathogen identification and disease management.
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Affiliation(s)
- Vimla Singh
- Department of Botany and Plant Physiology, Chaudhary Charan Singh Haryana Agricultural University, Regional Research Station, Karnal 132001, India
| | - Dilip K Lakshman
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Daniel P Roberts
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - Adnan Ismaiel
- Sustainable Agricultural Systems Laboratory, U.S. Department of Agriculture, Agricultural Research Service, Beltsville, MD 20705, U.S.A
| | - K S Hooda
- Germplasm Evaluation Division, Indian Council of Agricultural Research, National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Robin Gogoi
- Division of Plant Pathology, Indian Council of Agricultural Research, Indian Agricultural Research Institute, New Delhi 110012, India
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Jagan EG, Sharma P, Sureshkumar S, Pandi M. Isolation of Taxol and Flavin-like fluorochrome from Endophytic Fungi of Mangifera indica. J Pure Appl Microbiol 2021; 15:2195-2208. [DOI: 10.22207/jpam.15.4.43] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Scouting for novel and plant-derived biomolecules from endophytic microbial sources draws greater focus on the discovery of novel bioactive metabolites. With this rationale, we scouted the endophytic fungi for taxol, an anticancer diterpenoid and fluorescent biomolecules. In the present study, about 31 endophytic fungal isolates recovered from the Mangifera indica leaves were screened for taxol production in M1D medium. About five isolates were shortlisted based on the thin layer chromatographic analysis of the fungal extracts. Among them Colletotrichum sp. MIP-5 has been identified as a producer of fungal taxol based on UV, FTIR, TLC and HPLC analysis. The partially purified fungal taxol showed similar spectral and chromatographic features of commercially available paclitaxel. In addition to this, we also report the production of a fluorescent compound by Penicillium sp. MIP-3. The Flavin-like compound exhibited a bright greenish-yellow fluorescence with an emission maximum in the range of 505 – 545nm. GC-MS analysis showed the occurrence of Latia luciferin, primarily associated with the bioluminescence of freshwater limpet Latia neritoides. This is the first report of this compound from Penicillium sp. In addition, therapeutically active steroid (β-Sitosterol, Stigmasterol, Campesterol), quinones (Benzo[h]quinoline, 2,4-dimethyl-) and phloroglucinol (Aspidinol) derivatives were also identified from Penicillium sp. MIP-3 based on GC-MS analysis. These molecules could potentially be used in biological and pharmaceutical applications in future.
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Rai N, Kumari Keshri P, Verma A, Kamble SC, Mishra P, Barik S, Kumar Singh S, Gautam V. Plant associated fungal endophytes as a source of natural bioactive compounds. Mycology 2021; 12:139-159. [PMID: 34552808 PMCID: PMC8451683 DOI: 10.1080/21501203.2020.1870579] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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] [Indexed: 01/19/2023] Open
Abstract
Endophytes are a potent source of bioactive compounds that mimic plant-based metabolites. The relationship of host plant and endophyte is significantly associated with alteration in fungal colonisation and the extraction of endophyte-derived bioactive compounds. Screening of fungal endophytes and their relationship with host plants is essential for the isolation of bioactive compounds. Numerous bioactive compounds with antioxidant, antimicrobial, anticancer, and immunomodulatory properties are known to be derived from fungal endophytes. Bioinformatics tools along with the latest techniques such as metabolomics, next-generation sequencing, and metagenomics multilocus sequence typing can potentially fill the gaps in fungal endophyte research. The current review article focuses on bioactive compounds derived from plant-associated fungal endophytes and their pharmacological importance. We conclude with the challenges and opportunities in the research area of fungal endophytes.
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Affiliation(s)
- Nilesh Rai
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Priyanka Kumari Keshri
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Ashish Verma
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Swapnil C Kamble
- Department of Technology, Savitribai Phule Pune University, Ganeshkhind, Pune, India
| | - Pradeep Mishra
- Division of Biochemistry, Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Suvakanta Barik
- Chemical Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gandhinagar, Gujarat, India
| | - Santosh Kumar Singh
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | - Vibhav Gautam
- Centre of Experimental Medicine and Surgery, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Li H, Chen X, Qiu X, Huang W, Yang C. Comparison of Droplet Digital Polymerase Chain Reaction (ddPCR) and Real-Time Quantitative Polymerase Chain Reaction (qPCR) in Detecting Neonatal Invasive Fungal Infections. J BIOMATER TISS ENG 2021. [DOI: 10.1166/jbt.2021.2408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Invasive fungal infection (IFI) is the leading cause of death in neonatal patients, yet the diagnosis of IFI remains a major challenge. At present, most IFI laboratory diagnostic methods are based on classical, but limited, methods such as fungal isolation and culture and histopathological
examination. Recently, quantitative polymerase chain reaction (qPCR) and droplet digital polymerase chain reaction (ddPCR) technology have been adopted to quantify nucleic-acid identification. In this study, we established qPCR and ddPCR assays for IFI diagnosis and quantification. qPCR and
ddPCR were carried out using identical primers and probe for the amplification of 18S rRNA. Assay results for three fungal strains were positive, whereas ten non-fungal strains had negative results, indicating 100% specificity for both ddPCR and qPCR methods. Genomic DNA of Candida albicans
was tested after a serial dilution to compare the sensitivity of the two PCR methods. The limit of detection of ddPCR was 3.2 copies/L, which was a ten-fold increase compared with that of the qPCR method (32 copies/L). Blood samples from 127 patients with high-risk factors and clinical symptoms
for IFI were collected from a NICU in Shenzhen, China, and analyzed using qPCR and ddPCR. Thirty-four blood samples from neonates had a proven or probable diagnosis of IFI, and 25 of these were positive by qPCR, whereas 30 were positive by ddPCR. Among the 93 blood samples from neonates who
had a possible IFI or no IFI, 24 were positive using qPCR, and 7 were positive using ddPCR. In conclusion, ddPCR is a rapid and accurate pan-fungal detection method and provides a promising prospect for IFI clinical screening.
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Affiliation(s)
- Huitao Li
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Xueyu Chen
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Xiaomei Qiu
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
| | - Weimin Huang
- Department of Neonatology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, Guangdong, PR China
| | - Chuanzhong Yang
- Department of Neonatology, Affiliated Shenzhen Maternity & Child Healthcare Hospital, Southern Medical University, Shenzhen 518028, Guangdong, PR China
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Zhang W, Tian W, Gao Z, Wang G, Zhao H. Phylogenetic Utility of rRNA ITS2 Sequence-Structure under Functional Constraint. Int J Mol Sci 2020; 21:ijms21176395. [PMID: 32899108 PMCID: PMC7504139 DOI: 10.3390/ijms21176395] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [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: 08/12/2020] [Revised: 08/27/2020] [Accepted: 08/28/2020] [Indexed: 02/07/2023] Open
Abstract
The crucial function of the internal transcribed spacer 2 (ITS2) region in ribosome biogenesis depends on its secondary and tertiary structures. Despite rapidly evolving, ITS2 is under evolutionary constraints to maintain the specific secondary structures that provide functionality. A link between function, structure and evolution could contribute an understanding to each other and recently has created a growing point of sequence-structure phylogeny of ITS2. Here we briefly review the current knowledge of ITS2 processing in ribosome biogenesis, focusing on the conservative characteristics of ITS2 secondary structure, including structure form, structural motifs, cleavage sites, and base-pair interactions. We then review the phylogenetic implications and applications of this structure information, including structure-guiding sequence alignment, base-pair mutation model, and species distinguishing. We give the rationale for why incorporating structure information into tree construction could improve reliability and accuracy, and some perspectives of bioinformatics coding that allow for a meaningful evolutionary character to be extracted. In sum, this review of the integration of function, structure and evolution of ITS2 will expand the traditional sequence-based ITS2 phylogeny and thus contributes to the tree of life. The generality of ITS2 characteristics may also inspire phylogenetic use of other similar structural regions.
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Affiliation(s)
- Wei Zhang
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
- Correspondence: ; Tel.: +86-631-5688-303
| | - Wen Tian
- State Key Laboratory of Ballast Water Research, Comprehensive Technical Service Center of Jiangyin Customs, Jiangyin 214440, China;
| | - Zhipeng Gao
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
| | - Guoli Wang
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
| | - Hong Zhao
- Marine College, Shandong University, Weihai 264209, China; (Z.G.); (G.W.); (H.Z.)
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Polli AD, Ribeiro MADS, Garcia A, Polonio JC, Santos CM, Silva AA, Orlandelli RC, Castro JC, Abreu-Filho BA, Cabral MRP, Sarragiotto MH, Pamphile JA, Azevedo JL. Secondary metabolites of Curvularia sp. G6-32, an endophyte of Sapindus saponaria, with antioxidant and anticholinesterasic properties. Nat Prod Res 2020; 35:4148-4153. [DOI: 10.1080/14786419.2020.1739681] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Andressa Domingos Polli
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | | | - Adriana Garcia
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Julio Cesar Polonio
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Caroline Menicoze Santos
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Angela Aparecida Silva
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Ravely Casarotti Orlandelli
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - Juliana Cristina Castro
- Departamento de Ciências Básicas da Saúde, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | | | | | | | - João Alencar Pamphile
- Departamento de Biotecnologia, Genética e Biologia Celular, Universidade Estadual de Maringá, Maringá, PR, Brazil
| | - João Lúcio Azevedo
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz,” Universidade de São Paulo, Piracicaba, SP, Brazil
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