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Qin T, Ortega-Perez P, Wibbelt G, Lakim MB, Ginting S, Khoprasert Y, Wells K, Hu J, Jäkel T. A cyst-forming coccidian with large geographical range infecting forest and commensal rodents: Sarcocystis muricoelognathis sp. nov. Parasit Vectors 2024; 17:135. [PMID: 38491403 PMCID: PMC10943850 DOI: 10.1186/s13071-024-06230-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/03/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND The geographic distribution and host-parasite interaction networks of Sarcocystis spp. in small mammals in eastern Asia remain incompletely known. METHODS Experimental infections, morphological and molecular characterizations were used for discrimination of a new Sarcocystis species isolated from colubrid snakes and small mammals collected in Thailand, Borneo and China. RESULTS We identified a new species, Sarcocystis muricoelognathis sp. nov., that features a relatively wide geographic distribution and infects both commensal and forest-inhabiting intermediate hosts. Sarcocystis sporocysts collected from rat snakes (Coelognathus radiatus, C. flavolineatus) in Thailand induced development of sarcocysts in experimental SD rats showing a type 10a cyst wall ultrastructure that was identical with those found in Rattus norvegicus from China and the forest rat Maxomys whiteheadi in Borneo. Its cystozoites had equal sizes in all intermediate hosts and locations, while sporocysts and cystozoites were distinct from other Sarcocystis species. Partial 28S rRNA sequences of S. muricoelognathis from M. whiteheadi were largely identical to those from R. norvegicus in China but distinct from newly sequenced Sarcocystis zuoi. The phylogeny of the nuclear 18S rRNA gene placed S. muricoelognathis within the so-called S. zuoi complex, including Sarcocystis attenuati, S. kani, S. scandentiborneensis and S. zuoi, while the latter clustered with the new species. However, the phylogeny of the ITS1-region confirmed the distinction between S. muricoelognathis and S. zuoi. Moreover, all three gene trees suggested that an isolate previously addressed as S. zuoi from Thailand (KU341120) is conspecific with S. muricoelognathis. Partial mitochondrial cox1 sequences of S. muricoelognathis were almost identical with those from other members of the group suggesting a shared, recent ancestry. Additionally, we isolated two partial 28S rRNA Sarcocystis sequences from Low's squirrel Sundasciurus lowii that clustered with those of S. scandentiborneensis from treeshews. CONCLUSIONS Our results provide strong evidence of broad geographic distributions of rodent-associated Sarcocystis and host shifts between commensal and forest small mammal species, even if the known host associations remain likely only snapshots of the true associations.
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Affiliation(s)
- Tao Qin
- School of Ecology and Environmental Sciences and Yunnan International Joint Laboratory of Virology & Immunity, Yunnan University, Kunming, China
| | - Paula Ortega-Perez
- Department of Pathology, AnaPath Services GmbH, Liestal, Switzerland
- Department Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | - Gudrun Wibbelt
- Department Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research, Berlin, Germany
| | | | | | - Yuvaluk Khoprasert
- Department of Agriculture, Plant Protection Research and Development Office, Bangkok, Thailand
| | - Konstans Wells
- Department of Biosciences, Swansea University, Swansea, UK
| | - Junjie Hu
- School of Ecology and Environmental Sciences and Yunnan International Joint Laboratory of Virology & Immunity, Yunnan University, Kunming, China.
| | - Thomas Jäkel
- Department of Agriculture, Plant Protection Research and Development Office, Bangkok, Thailand.
- Institute of Biology, Department of Parasitology, University of Hohenheim, Stuttgart, Germany.
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Jäkel T, Raisch L, Richter S, Wirth M, Birenbaum D, Ginting S, Khoprasert Y, Mackenstedt U, Wassermann M. Morphological and molecular phylogenetic characterization of Sarcocystis kani sp. nov. and other novel, closely related Sarcocystis spp. infecting small mammals and colubrid snakes in Asia. Int J Parasitol Parasites Wildl 2023; 22:184-198. [PMID: 37915771 PMCID: PMC10615900 DOI: 10.1016/j.ijppaw.2023.10.005] [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: 06/07/2023] [Revised: 08/24/2023] [Accepted: 10/09/2023] [Indexed: 11/03/2023]
Abstract
We investigated the morphology and phylogenetic relationships of novel and previously recognized Sarcocystis spp. infecting small mammals and colubrid snakes in Asia. The nuclear 18S rRNA and mitochondrial cox1 of Sarcocystis sp.1 from mangrove snakes (Boiga dendrophila) in Thailand and Sarcocystis sp.2 from a ricefield rat (Rattus argentiventer) in Sumatra were partially sequenced. Sporocysts of Sarcocystis sp.1 induced development of sarcocysts in experimentally infected rats, which showed a unique ultrastructure that was observed previously by S.P. Kan in rats from Malaysia; therefore, we describe this species as Sarcocystis kani sp. nov. Its integration into the 18S rRNA phylogeny of Sarcocystis spp. cycling between small mammals and colubrid snakes helped clarify relationships among the so-called S. zuoi-complex of molecularly cryptic species: Sarcocystis kani sp. nov., S. sp.2, S. attenuati, S. scandentiborneensis, and S. zuoi were all included in this clade. Tree topology was resolved into dichotomies congruent with the morphological disparities between the taxa. However, cox1 gene sequencing (including newly sequenced S. singaporensis and S. zamani) revealed that Sarcocystis kani, S. attenuati, and S. scandentiborneensis were identical suggesting a recent, common ancestry. To identify other distinctive features, lineage-specific molecular patterns within both genes were examined revealing that all 18S rRNA sequences of the S. zuoi - complex possess a unique, 7-nt long motif in helix 38 of domain V7 that was different in S. clethrionomyelaphis which branched off basally from the complex. Three-dimensional homology modelling of COX1 protein structure identified amino acid substitutions within the barcode area specific for the S. zuoi-complex and substantial divergence in structurally important amino acids between Sarcocystis species of snakes as definitive hosts and other lineages of the Sarcocystidae. We discuss the utility of selected genes for species delimitation of the Sarcocystis spp. under investigation, which probably evolved during recent radiations of their intermediate and definitive hosts.
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Affiliation(s)
- Thomas Jäkel
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
- Department of Agriculture, Plant Protection Research and Development Office, Bangkok, Thailand
| | - Lisa Raisch
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
| | - Sarah Richter
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
| | - Mareike Wirth
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
| | - Damaris Birenbaum
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
| | | | - Yuvaluk Khoprasert
- Department of Agriculture, Plant Protection Research and Development Office, Bangkok, Thailand
| | - Ute Mackenstedt
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
| | - Marion Wassermann
- University of Hohenheim, Institute of Biology, Department of Parasitology, Stuttgart, Germany
- University of Hohenheim, Center of Biodiversity and Integrative Taxonomy, Stuttgart, Germany
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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] [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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Mohanty S, Mishra BK, Dasgupta M, Acharya GC, Singh S, Naresh P, Bhue S, Dixit A, Sarkar A, Sahoo MR. Deciphering phenotyping, DNA barcoding, and RNA secondary structure predictions in eggplant wild relatives provide insights for their future breeding strategies. Sci Rep 2023; 13:13829. [PMID: 37620406 PMCID: PMC10449851 DOI: 10.1038/s41598-023-40797-z] [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: 12/24/2022] [Accepted: 08/16/2023] [Indexed: 08/26/2023] Open
Abstract
Eggplant or aubergine (Solanum melongena L.) and its wild cousins, comprising 13 clades with 1500 species, have an unprecedented demand across the globe. Cultivated eggplant has a narrow molecular diversity that hinders eggplant breeding advancements. Wild eggplants need resurgent attention to broaden eggplant breeding resources. In this study, we emphasized phenotypic and genotypic discriminations among 13 eggplant species deploying chloroplast-plastid (Kim matK) and nuclear (ITS2) short gene sequences (400-800 bp) at DNA barcode region followed by ITS2 secondary structure predictions. The identification efficiency at the Kim matK region was higher (99-100%) than in the ITS2 region (80-90%). The eggplant species showed 13 unique secondary structures with a central ring with various helical orientations. Principal component analysis (PCoA) provides the descriptor-wise phenotypic clustering, which is essential for trait-specific breeding. Groups I and IV are categorized under scarlet complexes S. aethiopicum, S. trilobatum, and S. melongena (wild and cultivated). Group II represented the gboma clade (S. macrocarpon, S. wrightii, S. sisymbriifolium, and S. aculeatissimum), and group III includes S. mammosum, and S. torvum with unique fruit shape and size. The present study would be helpful in genetic discrimination, biodiversity conservation, and the safe utilization of wild eggplants.
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Affiliation(s)
- Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
- Department of Molecular Biology and Biotechnology, Institute of Agricultural Sciences (IAS), Siksha O Anusandhan, Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Bandana Kumari Mishra
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India
| | - Madhumita Dasgupta
- ICAR Research Complex for Northeastern Hill Region, Manipur Centre, Imphal, Manipur, 795004, India
- Department of Molecular Biology and Biotechnology, Institute of Agricultural Sciences (IAS), Siksha O Anusandhan, Deemed to be University, Bhubaneswar, Odisha, 751003, India
| | - Gobinda Chandra Acharya
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
| | - Satyapriya Singh
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India
| | - Ponnam Naresh
- ICAR-Indian Institute of Horticultural Research, Bengaluru, 560089, Karnataka, India
| | - Shyamlal Bhue
- Institute of Life Sciences, Bhubaneswar, Odisha, 751024, India
| | - Anshuman Dixit
- Institute of Life Sciences, Bhubaneswar, Odisha, 751024, India
| | - Arup Sarkar
- Trident Academy of Creative Technology, Bhubaneswar, Odisha, 751024, India
| | - Manas Ranjan Sahoo
- Central Horticultural Experiment Station, ICAR-Indian Institute of Horticultural Research, Bhubaneswar, Odisha, 751019, India.
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Devi MP, Dasgupta M, Mohanty S, Sharma SK, Hegde V, Roy SS, Renadevan R, Kumar KB, Patel HK, Sahoo MR. DNA Barcoding and ITS2 Secondary Structure Predictions in Taro ( Colocasia esculenta L. Schott) from the North Eastern Hill Region of India. Genes (Basel) 2022; 13:genes13122294. [PMID: 36553561 PMCID: PMC9778394 DOI: 10.3390/genes13122294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 10/28/2022] [Accepted: 11/01/2022] [Indexed: 12/12/2022] Open
Abstract
Taro (Colocasia esculenta L. Schott, Araceae), an ancient root and tuber crop, is highly polygenic, polyphyletic, and polygeographic in nature, which leads to its rapid genetic erosion. To prevent the perceived loss of taro diversity, species discrimination and genetic conservation of promising taro genotypes need special attention. Reports on genetic discrimination of taro at its center of origin are still untapped. We performed DNA barcoding of twenty promising genotypes of taro indigenous to the northeastern hill region of India, deploying two chloroplast-plastid genes, matK and rbcL, and the ribosomal nuclear gene ITS2. The secondary structure of ITS2 was determined and molecular phylogeny was performed to assess genetic discrimination among the taro genotypes. The matK and rbcL genes were highly efficient (>90%) in amplification and sequencing. However, the ITS2 barcode region achieved significant discrimination among the tested taro genotypes. All the taro genotypes displayed most similar sequences at the conserved matK and rbcL loci. However, distinct sequence lengths were observed in the ITS2 barcode region, revealing accurate discriminations among the genotypes. Multiple barcode markers are unrelated to one another and change independently, providing different estimations of heritable traits and genetic lineages; thus, they are advantageous over a single locus in genetic discrimination studies. A dynamic programming algorithm that used base-pairing interactions within a single nucleic acid polymer or between two polymers transformed the secondary structures into the symbol code data to predict seven different minimum free energy secondary structures. Our analysis strengthens the potential of the ITS2 gene as a potent DNA barcode candidate in the prediction of a valuable secondary structure that would help in genetic discrimination between the genotypes while augmenting future breeding strategies in taro.
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Affiliation(s)
- Mayengbam Premi Devi
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- College of Agriculture, Central Agricultural University (CAU-Imphal), Kyrdemkulai 793105, India
| | - Madhumita Dasgupta
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
| | - Susheel Kumar Sharma
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- ICAR—Indian Agricultural Research Institute, Pusa Campus, New Delhi 110012, India
| | - Vivek Hegde
- ICAR—Central Tuber Crops Research Institute, Thiruvananthapuram 695017, India
- ICAR—Indian Institute of Horticultural Research, Bengaluru 560089, India
| | - Subhra Saikat Roy
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
| | - Rennya Renadevan
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
| | | | - Hitendra Kumar Patel
- Centre for Cellular and Molecular Biology, Hyderabad 570007, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
| | - Manas Ranjan Sahoo
- Indian Council of Agricultural Research (ICAR) Research Complex for North Eastern Hill Region, Imphal 795004, India
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, India
- Correspondence: (H.K.P.); (M.R.S.); Tel.: +91-674-247-1867 (M.R.S.); Fax: +91-674-247-1712 (M.R.S.)
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Acharya GC, Mohanty S, Dasgupta M, Sahu S, Singh S, Koundinya AVV, Kumari M, Naresh P, Sahoo MR. Molecular Phylogeny, DNA Barcoding, and ITS2 Secondary Structure Predictions in the Medicinally Important Eryngium Genotypes of East Coast Region of India. Genes (Basel) 2022; 13:genes13091678. [PMID: 36140845 PMCID: PMC9498504 DOI: 10.3390/genes13091678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 09/15/2022] [Accepted: 09/15/2022] [Indexed: 11/16/2022] Open
Abstract
Commercial interest in the culinary herb, Eryngium foetidum L., has increased worldwide due to its typical pungency, similar to coriander or cilantro, with immense pharmaceutical components. The molecular delimitation and taxonomic classification of this lesser-known medicinal plant are restricted to conventional phenotyping and DNA-based marker evaluation, which hinders accurate identification, genetic conservation, and safe utilization. This study focused on species discrimination using DNA sequencing with chloroplast–plastid genes (matK, Kim matK, and rbcL) and the nuclear ITS2 gene in two Eryngium genotypes collected from the east coast region of India. The results revealed that matK discriminated between two genotypes, however, Kim matK, rbcL, and ITS2 identified these genotypes as E. foetidum. The ribosomal nuclear ITS2 region exhibited significant inter- and intra-specific divergence, depicted in the DNA barcodes and the secondary structures derived based on the minimum free energy. Although the efficiency of matK genes is better in species discrimination, ITS2 demonstrated polyphyletic phylogeny, and could be used as a reliable marker for genetic divergence studies understanding the mechanisms of RNA molecules. The results of this study provide insights into the scientific basis of species identification, genetic conservation, and safe utilization of this important medicinal plant species.
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Affiliation(s)
- Gobinda Chandra Acharya
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Sansuta Mohanty
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Madhumita Dasgupta
- ICAR Research Complex for Northeastern Hill Region, Manipur Centre, Imphal 795004, Manipur, India
| | - Supriya Sahu
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
- All India Institute of Medical Sciences, Bhubaneswar 751019, Odisha, India
| | - Satyapriya Singh
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Ayyagari V. V. Koundinya
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
| | - Meenu Kumari
- ICAR Research Complex for Eastern Region, Research Centre, Ranchi 834010, Jharkhand, India
| | - Ponnam Naresh
- ICAR–Indian Institute of Horticultural Research, Bengaluru 560089, Karnataka, India
| | - Manas Ranjan Sahoo
- Central Horticultural Experiment Station, ICAR–Indian Institute of Horticultural Research, Bhubaneswar 751019, Odisha, India
- Correspondence: ; Tel.: +91-674-2471867; Fax: +91-674-2471712
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Talukdar R, Padhi S, Rai AK, Masi M, Evidente A, Jha DK, Cimmino A, Tayung K. Isolation and Characterization of an Endophytic Fungus Colletotrichum coccodes Producing Tyrosol From Houttuynia cordata Thunb. Using ITS2 RNA Secondary Structure and Molecular Docking Study. Front Bioeng Biotechnol 2021; 9:650247. [PMID: 34222209 PMCID: PMC8249321 DOI: 10.3389/fbioe.2021.650247] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 05/17/2021] [Indexed: 11/13/2022] Open
Abstract
An endophytic fungus isolated from healthy leaf tissues of Houttuynia cordata Thunb., an ethnomedicinal plant of North East India, showed a considerable amount of antimicrobial activity. The ethyl acetate extract of the fungal culture filtrates displayed promising antimicrobial activity against a panel of clinically significant pathogens including Candida albicans, Staphylococcus aureus, Escherichia coli, and Pseudomonas aeruginosa. Bioassay guided purification of the organic extract using column and thin layer chromatography yielded a pure homogenous compound which was identified using spectroscopic methods (essentially by 1H NMR and MS) as tyrosol, a well-known phenylethanoid present in several natural sources. Besides, molecular docking studies against tyrosyl tRNA synthetases (TyrRS) of S. aureus (PDB ID: 1JIL) and E. coli (PDB ID: 1VBM), and CYP45014α-lanosterol demethylase (CYP51) of C. albicans (PDB ID: 5FSA) revealed tyrosol has a strong binding affinity with the enzyme active site residues. The fungus was identified as Colletotrichum sp. and characterized by its genomic ITS rDNA and ITS2 sequences. Phylogenetic analyses showed clustering of our isolate with Colletotrichum coccodes. Species of Colletotrichum are also reported to be plant pathogens. Therefore, to confirm the endophytic lifestyle of the isolate, ITS2 RNA secondary structure study was undertaken. The result indicated our isolate exhibited differences in the folding pattern as well as in motif structures when compared to those of pathogenic C. coccodes. The findings indicated that endophytic fungi harboring H. cordata could be explored as a potent source of antimicrobial agents.
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Affiliation(s)
- Rajreepa Talukdar
- Mycology and Plant Pathology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | - Amit K Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | - Marco Masi
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Antonio Evidente
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Dhruva Kumar Jha
- Mycology and Plant Pathology Laboratory, Department of Botany, Gauhati University, Guwahati, India
| | - Alessio Cimmino
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Kumananda Tayung
- Mycology and Plant Pathology Laboratory, Department of Botany, Gauhati University, Guwahati, India
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Limon T, Birke A, Monribot-Villanueva JL, Guerrero-Analco JA, Altúzar-Molina A, Carrión G, Goycoolea FM, Moerschbacher BM, Aluja M. Chitosan coatings reduce fruit fly (Anastrepha obliqua) infestation and development of the fungus Colletotrichum gloeosporioides in Manila mangoes. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2021; 101:2756-2766. [PMID: 33150630 DOI: 10.1002/jsfa.10903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/07/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Mangoes are tropical fruits appreciated worldwide but are extremely perishable, being susceptible to decay, pest infestation and fungal diseases. Using the flavorful and highly valued 'Manila' cultivar, we examined the effect of second-generation chitosan coatings on shelf-life, phenolic compound variation, phytohormones, pest infestation by fruit flies (Anastrepha obliqua) and anthracnose disease caused by the fungus Colletotrichum gloeosporioides. RESULTS We observed almost total elimination of A. obliqua eggs with 10 and 20 g L-1 chitosan in diluted acetic acid and a five- to sixfold reduction in anthracnose damage. Treatment with 20 g L-1 chitosan also extended the shelf-life. External (skin) and internal (pulp) discoloration processes were delayed. Fruit firmness was higher when compared with control and acetic acid treatments, and total soluble solids were lower in chitosan-treated fruit. Targeted and non-targeted metabolomics analyses on chitosan-coated fruit identified some phenolic compounds related to the tannin pathway. In addition, abscisic acid and jasmonic acid in the peel were downregulated in chitosan-coated mango peels. Both phytohormones and phenolic content may explain the reduced susceptibility of mangoes to anthracnose development and A. obliqua egg eclosion or larval development. CONCLUSIONS We conclude that chitosan coatings represent an effective postharvest treatment that significantly reduces anthracnose disease, inhibits A. obliqua egg eclosion and significantly extends 'Manila' mango shelf-life, a key factor currently inhibiting large-scale commercialization of this valuable fruit. © 2020 Society of Chemical Industry.
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Affiliation(s)
- Tamara Limon
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, Münster, 48143, Germany
| | - Andrea Birke
- Red de Manejo Biorracional de Plagas y Vectores, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91073, Mexico
| | - Juan Luis Monribot-Villanueva
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91073, Mexico
| | - José Antonio Guerrero-Analco
- Red de Estudios Moleculares Avanzados, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91073, Mexico
| | - Alma Altúzar-Molina
- Red de Manejo Biorracional de Plagas y Vectores, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91073, Mexico
| | - Gloria Carrión
- Red de Biodiversidad y Sistemática, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Xalapa, 91073, Mexico
| | - Francisco M Goycoolea
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, Münster, 48143, Germany
- School of Food Science and Nutrition, University of Leeds, Leeds, UK
| | - Bruno M Moerschbacher
- Institute for Biology and Biotechnology of Plants, University of Münster, Schlossplatz 8, Münster, 48143, Germany
| | - Martín Aluja
- Red de Manejo Biorracional de Plagas y Vectores, Clúster Científico y Tecnológico Biomimic®, Instituto de Ecología, A.C. (INECOL), Carretera antigua a Coatepec No. 351, El Haya, Xalapa, Veracruz, 91073, Mexico
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9
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Gong L, Shi W, Yang M, Luo H. Variations in the conserved 18S and 5.8S reveal the putative pseudogenes in 18S-ITS1-5.8S rDNA of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae). Biochem Biophys Res Commun 2020; 534:233-239. [PMID: 33276952 DOI: 10.1016/j.bbrc.2020.11.106] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 11/26/2022]
Abstract
Many early studies of ribosomal RNA gene (rDNA) suggested that rDNA tandem repeats within species are homogeneous. However, increasing number of reports have found intra-individual rDNA polymorphism across a range of taxa. Here, we reported a high level of intra-individual polymorphism of 18S-ITS1-5.8S rDNA in the genome of Cynoglossus melampetalus (Pleuronectiformes: Cynoglossidae), indicating a non-concerted evolution manner. Sequence alignments found two distinct types of 18S and 5.8S (Type A and B) and five types of ITS1 sequence (Type A - E) coexisted in the genome differing in length, GC content, secondary structure stability and minimum free energy. Based on the unique features of pseudogene and comparison of the conserved 18S rDNA sequence and 5.8S secondary structure of 22 flatfishes revealed that Type B sequences of 18S, 5.8S and their linked ITS1 were putative pseudogenes. So far, detection of rRNA pseudogenes from the multiple rDNA copies has been an intricate puzzle. Our results, as a result, provide a new ideal for rRNA pseudogene identification.
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Affiliation(s)
- Li Gong
- National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Marine Science and Technology College, Zhejiang Ocean University, 316022, Zhoushan, China; Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry, Guangxi Beibu Gulf Marine Research Center, Guangxi Academy of Sciences, Nanning, 530007, China.
| | - Wei Shi
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Min Yang
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
| | - Hairong Luo
- Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, China
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10
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Tasneem F, Shakoori FR, Ilyas M, Shahzad N, Potekhin A, Shakoori AR. Genetic diversity of Paramecium species on the basis of multiple loci analysis and ITS secondary structure models. J Cell Biochem 2020; 121:3837-3853. [PMID: 31692070 DOI: 10.1002/jcb.29546] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 10/21/2019] [Indexed: 01/24/2023]
Abstract
Among ciliates, Paramecium has become a privileged model for the study of "species problem" particularly in the case of the "Paramecium aurelia complex" that has been intensely investigated. Despite extensive studies, the taxonomy of Paramecium is still challenging. The major problem is an uneven sampling of Paramecium with relatively few representatives of each species. To investigate species from the less discovered region (Pakistan), 10 isolates of Paramecium species including a standing-alone FT8 strain previously isolated by some of us were subjected to molecular characterization. Fragments of 18S recombinant DNA (rDNA), ITS1-5.8S-ITS2-5'LSU rDNA, cytochrome c oxidase subunit II, and hsp70 genes were used as molecular markers for phylogenetic analysis of particular isolates. The nucleotide sequences of polymerase chain reaction products of all markers were compared with the available sequences of relevant markers of other Paramecium species from GenBank. Phylogenetic trees based on all molecular markers showed that all the nine strains had a very close relationship with Paramecium primaurelia except for the FT8 strain. FT8 consistently showed its unique position in comparison to all other species in the phylogenetic trees. Available sequences of internal transcribed spacer 1 (ITS1) and ITS2 and some other ciliate sequences from GenBank were used for the construction of secondary models. Two highly conserved helices supported by compensatory base changes among all ciliates of ITS2 secondary structures were found similar to other eukaryotes. Therefore, the most conserved 120 to 180 base pairs regions were identified for their comparative studies. We found that out of the three helices in ITS1 structure, helix B was more conserved in Paramecium species. Despite various substitutions in the primary sequence, it was observed that secondary structures of ITS1 and ITS2 could be helpful in interpreting the phylogenetic relationships both at species as well as at generic level.
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Affiliation(s)
- Fareeda Tasneem
- Department of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
| | - Farah R Shakoori
- Department of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
| | - Muhammad Ilyas
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
| | - Naveed Shahzad
- School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
| | - Alexey Potekhin
- Department of Microbiology, Faculty of Biology, Saint Petersburg State University, Saint Petersburg, Russia
| | - Abdul R Shakoori
- Department of Zoology, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan.,School of Biological Sciences, University of the Punjab, Quaid-i-Azam Campus, Lahore, Pakistan
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11
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de Souza TB, Gaeta ML, Martins C, Vanzela ALL. IGS sequences in Cestrum present AT- and GC-rich conserved domains, with strong regulatory potential for 5S rDNA. Mol Biol Rep 2019; 47:55-66. [PMID: 31571109 DOI: 10.1007/s11033-019-05104-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 09/24/2019] [Indexed: 11/28/2022]
Abstract
The 35S and 5S ribosomal DNA (rDNA) organized in thousands of copies in genomes, have been widely used in numerous comparative cytogenetic studies. Nevertheless, several questions related to the diversity and organization of regulatory motifs in 5S rDNA remain to be addressed. The 5S rDNA unit is composed of a conserved 120 bp length coding region and an intergenic spacer (IGS) containing potential regulatory motifs (Poly-T, AT-rich and GC-rich) differing in number, redundancy and position along the IGS. The Cestrum species (Solanaceae) have large genomes (about 10 pg/1C) and conserved 2n = 16 karyotypes. Strikingly, these genomes show high diversity of heterochromatin distribution, variability in 35S rDNA loci and the occurrence of B chromosomes. However, the 5S rDNA loci are highly conserved in the proximal region of chromosome 8. Comparison of seventy-one IGS sequences in plants revealed several conserved motifs with potential regulatory function. The AT- and GC-rich domains appeared highly conserved in Cestrum chromosomes. The 5S genic and the GC-rich IGS probe produced FISH signals in both A (pair 8) and B chromosomes. The GC-rich domain presented a strong potential for regulation because it may be associated with CpG islands organization, as well as to hairpin and loop organization. Another interesting aspect was the ability of AT- and GC-rich motifs to produce non-heterochromatic CMA/DAPI signals. While the length of the 5S rDNA IGS region varied in size between the Cestrum species, the individual sequence motifs seem to be conserved suggesting their regulatory function. The most striking feature was the conserved GC-rich domain in Cestrum, which is recognized as a signature trait of the proximal region of chromosome pair 8.
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Affiliation(s)
- Thaíssa Boldieri de Souza
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil
| | - Marcos Letaif Gaeta
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil
| | - Cesar Martins
- Departamento de Morfologia, Instituto de Biociências, Universidade Estadual Paulista (UNESP), Botucatu, SP, CEP 18618689, Brazil
| | - André Luís Laforga Vanzela
- Laboratório de Citogenética e Diversidade Vegetal, Departamento de Biologia Geral, Centro de Ciências Biológicas, Universidade Estadual de Londrina, Londrina, Paraná, 86057-970, Brazil.
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12
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Garjito TA, Widiastuti U, Mujiyono M, Prihatin MT, Widiarti W, Setyaningsih R, Alfiah S, Widartono BS, Syafruddin D, Satoto TBT, Gavotte L, Bangs MJ, Manguin S, Frutos R. Genetic homogeneity of Anopheles maculatus in Indonesia and origin of a novel species present in Central Java. Parasit Vectors 2019; 12:351. [PMID: 31307517 PMCID: PMC6631912 DOI: 10.1186/s13071-019-3598-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 07/05/2019] [Indexed: 11/16/2022] Open
Abstract
Background Anopheles maculatus (s.s.) is an important vector of malaria in Indonesia. Previously it was considered the only member of the Maculatus Group present in Indonesia. A novel species was recently identified in the Kulon Progo District in Central Java. Until recently, few investigations have been conducted looking at An. maculatus genetic diversity in Indonesia, including allopatric island populations. Methods Indonesian An. maculatus (s.l.) samples were collected in several locations in Java, Lesser Sunda Island group, Sumatra and in Kulon Progo (Yogyakarta, central Java) where a novel species has been identified. Samples from a 30-year-old colony of the Kulon Progo population were also included in the analysis. Maximum-likelihood analysis established the phylogenies of the ITS2 (nuclear) and cox1 (mitochondrial) markers. Putative times of separation were based on cox1 genetic distances. Results Two species of the Maculatus Group are present in Indonesia. The novel sibling species is more closely related to Anopheles dispar than to An. maculatus (s.s.). Anopheles maculatus (s.s.) samples are homogeneous based on the ITS2 sequences. Indonesian samples and An. dispar belong to the same cox1 maternal lineage and differ from all other known members of the Maculatus Group. Divergence time between the different populations found in Java was estimated using an established cox1 mutation rate. Conclusions A novel species within the Maculatus Group, most closely related to An. dispar, is confirmed present in the Kulon Progo area of Central Java. The divergence of this species from An. maculatus (s.s.) is explained by the stable refugia in the Kulon Progo area during the quaternary period of intense volcanic activity throughout most of Java. This novel species awaits detailed morphological description before applying a formal species name. For the interim, it is proposed that the Kulon Progo population be designated An. maculatus var. menoreh to distinguish it from An. maculatus (s.s.). Electronic supplementary material The online version of this article (10.1186/s13071-019-3598-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Triwibowo Ambar Garjito
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia. .,University of Montpellier, Montpellier, France. .,HydroSciences Montpellier (UMR-HSM), Institut de Recherche pour le Développement (IRD France), CNRS, Montpellier, France.
| | - Umi Widiastuti
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Mujiyono Mujiyono
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Mega Tyas Prihatin
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Widiarti Widiarti
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Riyani Setyaningsih
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Siti Alfiah
- Institute for Vector and Reservoir Control Research and Development, National Institute of Health Research and Development, The Ministry of Health of Indonesia, Salatiga, Central Java, Indonesia
| | - Barandi Sapta Widartono
- Department of Geographical Information System, Faculty of Geography, Gadjah Mada University, Yogyakarta, Indonesia
| | - Din Syafruddin
- Eijkman Institute for Molecular Biology, Jakarta, Indonesia
| | - Tri Baskoro Tunggul Satoto
- Department of Parasitology, Faculty of Medicine, Public Health and Nursing, Gadjah Mada University, Yogyakarta, Indonesia
| | | | - Michael J Bangs
- Public Health & Malaria Control, International SOS/PT. Freeport Indonesia, Kuala Kencana, Indonesia.,Department of Entomology, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Sylvie Manguin
- University of Montpellier, Montpellier, France.,HydroSciences Montpellier (UMR-HSM), Institut de Recherche pour le Développement (IRD France), CNRS, Montpellier, France
| | - Roger Frutos
- University of Montpellier, Montpellier, France.,IES, University of Montpellier, CNRS, Montpellier, France.,Cirad, UMR 17, Intertryp, Montpellier, France
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13
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Sundaresan N, Sahu AK, Jagan EG, Pandi M. Evaluation of ITS2 molecular morphometrics effectiveness in species delimitation of Ascomycota - A pilot study. Fungal Biol 2019; 123:517-527. [PMID: 31196521 DOI: 10.1016/j.funbio.2019.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 04/01/2019] [Accepted: 05/02/2019] [Indexed: 01/19/2023]
Abstract
Exploring the secondary structure information of nuclear ribosomal internal transcribed spacer 2 (ITS2) has been a promising approach in species delimitation. However, Compensatory base changes (CBC) concept employed in this approach turns futile when CBC is absent. This prompted us to investigate the utility of insertion/deletion (INDELs) and substitutions in fungal delineation at species level. Upon this rationale, 116 strains representing 97 species, belonging to 6 genera (Colletotrichum, Boeremia, Leptosphaeria, Peyronellaea, Plenodomus and Stagonosporopsis) of Ascomycota were retrieved from Q-bank for molecular morphometric analysis. CBC, INDELs and substitutions between the species of their respective genus were recorded. Most species combinations lacked CBC. Among the substitution events, transitions were predominant. INDELs were less frequent than the substitutions. These evolutionary events were mapped upon the helices to discern species specific variation sites. In 68 species unique variation sites were recognised. The remaining 29 species shared absolute similarity with distinctly named species. The variation sites catalogued in them overlapped with other distinct species and resulted in the blurring of species boundaries. Species specific variation sites recognized in this study are the preliminary results and they could be discerned with absolute confidence when larger datasets encompassing all described species of genera were investigated. They could be of potential use in barcoding fungi at species level. This study also concludes that the ITS2 molecular morphometric analysis is an efficient third dimensional study of the fungal species delimitation. This may help to avoid the false positives in species delimitations and to alleviate the challenges in molecular characterization.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Amit Kumar Sahu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India.
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14
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Sundaresan N, Jagan EG, Kathamuthu G, Pandi M. Internal transcribed spacer 2 (ITS2) molecular morphometric analysis based species delimitation of foliar endophytic fungi from Aglaia elaeagnoidea, Flacourtia inermis and Premna serratifolia. PLoS One 2019; 14:e0215024. [PMID: 30964914 PMCID: PMC6456209 DOI: 10.1371/journal.pone.0215024] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 03/25/2019] [Indexed: 11/19/2022] Open
Abstract
Molecular morphometrics is an emerging third dimensional aspect of fungal species delimitation. They have been demonstrated to be more informative than conventional barcoding methods. Hence in this study, foliar endophytic fungal (FEF) assemblages in three Magnoliopsida plants were delimited using nuclear ribosomal internal transcribed spacer 2 (ITS2) sequence-secondary structural features based phylogenetic analysis, also known as molecular morphometrics. A total of 392 FEF isolates were obtained from the Aglaia elaeagnoidea, Flacourtia inermis, and Premna serratifolia leaves and grouped into 98 morphotypes. Among these host plants, P. serratifolia showed the maximum percentage of colonization frequency. Representatives of each morphotype was sequenced and subjected to further molecular characterization. The results revealed that morphotypes were belonged to the phylum of Ascomycota, distributed over two classes (Sordariomycetes (68.59%) and Dothideomycetes (31.41%)), 6 orders and 19 genera. Based on compensatory base changes (CBC) analysis and absolute identity of ITS2 structure, 21, 20 and 23 species were recognized from A. elaeagnoidea, F. inermis, and P. serratifolia respectively. Diversity indices were higher in A. elaeagnoidea, despite it accounted for a modest 16.8% of total isolates recorded in this study. The genus Colletotrichum was predominant in A. elaeagnoidea (39%) and P. serratifolia (48%). Similarly, Diaporthe (43%) was dominant in F. inermis. Several host-specific species were also observed. This study concludes that these plants host diverse species of Ascomycota. To the best of our knowledge, this is the first detailed report on FEF diversity from these plants. Also, the inclusion of ITS2 secondary structure information along with the sequence provides a further dimension to resolve the inherent problems in identification of fungal species.
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Affiliation(s)
- Natesan Sundaresan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Enthai Ganeshan Jagan
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - GokulRaj Kathamuthu
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
| | - Mohan Pandi
- Department of Molecular Microbiology, School of Biotechnology, Madurai Kamaraj University, Madurai, Tamil Nadu, India
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15
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Zhu S, Li Q, Chen S, Wang Y, Zhou L, Zeng C, Dong J. Phylogenetic analysis of Uncaria species based on internal transcribed spacer (ITS) region and ITS2 secondary structure. PHARMACEUTICAL BIOLOGY 2018; 56:548-558. [PMID: 30392423 PMCID: PMC6225500 DOI: 10.1080/13880209.2018.1499780] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/22/2018] [Accepted: 07/06/2018] [Indexed: 05/31/2023]
Abstract
CONTEXT The plant genus Uncaria (Rubiaceae), also known as Gouteng, is the source of an important traditional Chinese medicine. Misidentification and adulteration of Gouteng affect the safety and efficacy of the medication. Phylogenetic relationships among the species of this genus are unknown. OBJECTIVE The present study sought to detect the phylogenetic relationships based on internal transcribed spacer (ITS) region of all 12 species of Uncaria recorded in the Flora of China. MATERIALS AND METHODS Accession of seven species of Uncaria served as reference samples. ITS region was used for polymerase chain reaction (PCR) amplification of the reference samples representing 39 specimens. Distance analysis, species discrimination, and secondary structure of ITS2 were used to assess the ability of ITS sequence in authenticating. The phylogenetic relationships were detected using three methods: Bayesian inference (BI), maximum likelihood (ML), and neighbor joining (NJ). RESULTS Five species of traditional Chinese medicine Gouteng were well resolved in molecular phylogenetic tree. Besides, Uncaria lancifolia Hutch. was closer to U. rhynchophylloides F.C. How and U. sessilifructus Roxb. was closer to U. laevigata Wall. within the tree. Further, we also found that ITS2 secondary structure can be a candidate tool in distinguishing two closely related species U. yunnanensis K.C.Hsia and U. lanosa Wall. For accurate identification of different species of Uncaria based on species-specific nucleotide sites, a consensus sequences database with all 12 species is established. DISCUSSIONS AND CONCLUSIONS The results are able to discriminate Uncaria species and illustrate the phylogenetic relationships, which are essential for the investigation of adulterants and misidentifications of Uncaria.
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Affiliation(s)
- Shuang Zhu
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Qiwei Li
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Shanchong Chen
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Yesheng Wang
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Lin Zhou
- Center for Bioresources and Drug Discovery and School of Biosciences and Biopharmaceutics Guangdong Province Key Laboratory for Biotechnology Drug Candidates, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Changqing Zeng
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
| | - Jun Dong
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, People’s Republic of China
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16
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Kapoor N, Gambhir L, Saxena S. Secondary structure prediction of ITS rRNA region and molecular phylogeny: an integrated approach for the precise speciation of Muscodor species. ANN MICROBIOL 2018. [DOI: 10.1007/s13213-018-1381-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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17
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Sha SP, Suryavanshi MV, Jani K, Sharma A, Shouche Y, Tamang JP. Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages. Front Microbiol 2018; 9:2237. [PMID: 30319566 PMCID: PMC6169615 DOI: 10.3389/fmicb.2018.02237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Accepted: 09/03/2018] [Indexed: 12/25/2022] Open
Abstract
Marcha, thiat, dawdim, hamei, humao, khekhrii, chowan, and phut are traditionally prepared dried starters used for production of various ethnic alcoholic beverages in North East states of India. The surveillance of mycobiome associated with these starters have been revealed by culture-dependent methods using phenotypic and molecular tools. We identified Wickerhamomyces anomalus, Pichia anomala, Saccharomycopsis fibuligera, Pichia terricola, Pichia kudriavzevii, and Candida glabrata by ITS-PCR. The diversity of yeasts and molds in all 40 samples was also investigated by culture-independent method using PCR-DGGE analysis. The average distributions of yeasts showed Saccharomyces cerevisiae (16.5%), Saccharomycopsis fibuligera (15.3%), Wickerhamomyces anomalus (11.3%), S. malanga (11.7%), Kluyveromyces marxianus (5.3%), Meyerozyma sp. (2.7%), Candida glabrata (2.7%), and many strains below 2%. About 12 strains of molds were also identified based on PCR-DGGE analysis which included Aspergillus penicillioides (5.0%), Rhizopus oryzae (3.3%), and sub-phylum: Mucoromycotina (2.1%). Different techniques used in this paper revealed the diversity and differences of mycobiome species in starter cultures of India which may be referred as baseline data for further research.
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Affiliation(s)
- Shankar Prasad Sha
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
| | - Mangesh Vasant Suryavanshi
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India.,National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Kunal Jani
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Avinash Sharma
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Yogesh Shouche
- National Centre for Microbial Resource, National Centre for Cell Science, Pune, India
| | - Jyoti Prakash Tamang
- DAICENTRE (DBT-AIST International Centre for Translational and Environmental Research) and Bioinformatics Centre, Department of Microbiology, School of Life Sciences, Sikkim University, Gangtok, India
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18
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Gong L, Shi W, Yang M, Kong X. Marked intra-genomic variation and pseudogenes in the ITS1-5.8S-ITS2 rDNA of Symphurus plagiusa (Pleuronectiformes: Cynoglossidae). ANIM BIOL 2018. [DOI: 10.1163/15707563-17000134] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Abstract
The eukaryotic ribosomal DNA (rDNA) cluster consists of multiple copies of three genes (18S, 5.8S, and 28S rDNA) and two internal transcribed spacers (ITS1 and ITS2). In recent years, an increasing number of rDNA sequence polymorphisms have been identified in numerous species. In the present study, we provide 33 complete ITS (ITS1-5.8S-ITS2) sequences from two Symphurus plagiusa individuals. To the best of our knowledge, these sequences are the first detailed information on ITS sequences in Pleuronectiformes. Here, two divergent types (Type A and B) of the ITS1-5.8S-ITS2 rDNA sequence were found, which mainly differ in sequence length, GC content, nucleotide diversity (π), secondary structure and minimum free energy. The ITS1-5.8S-ITS2 rDNA sequence of Type B was speculated to be a putative pseudogene according to pseudogene identification criteria. Cluster analysis showed that sequences from the same type clustered into one group and two major groups were formed. The high degree of ITS1-5.8S-ITS2 sequence polymorphism at the intra-specific level indicated that the S. plagiusa genome has evolved in a non-concerted evolutionary manner. These results not only provide useful data for ribosomal pseudogene identification, but also further contribute to the study of rDNA evolution in teleostean genomes.
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Affiliation(s)
- Li Gong
- 1National Engineering Laboratory of Marine Germplasm Resources Exploration and Utilization, Zhejiang Ocean University, 316022, Zhoushan, China
- 2National Engineering Research Center for Facilitated Marine Aquaculture, Marine Science and Technology College, Zhejiang Ocean University, 316022, Zhoushan, China
| | - Wei Shi
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
| | - Min Yang
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
| | - Xiaoyu Kong
- 3Key Laboratory of Tropical Marine Bio-resources and Ecology, Guangdong Provincial Key Laboratory of Applied Marine Biology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, 510000, Guangzhou, China
- 4South China Sea Bio-Resource Exploitation and Utilization Collaborative Innovation Center, 510000, Guangzhou, China
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Liu Y, Erséus C. New specific primers for amplification of the Internal Transcribed Spacer region in Clitellata (Annelida). Ecol Evol 2017; 7:10421-10439. [PMID: 29238565 PMCID: PMC5723599 DOI: 10.1002/ece3.3212] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 06/05/2017] [Accepted: 06/06/2017] [Indexed: 11/11/2022] Open
Abstract
Nuclear molecular evidence, for example, the rapidly evolving Internal Transcribed Spacer region (ITS), integrated with maternally inherited (mitochondrial) COI barcodes, has provided new insights into the diversity of clitellate annelids. PCR amplification and sequencing of ITS, however, are often hampered by poor specificity of primers used. Therefore, new clitellate‐specific primers for amplifying the whole ITS region (ITS: 29F/1084R) and a part of it (ITS2: 606F/1082R) were developed on the basis of a collection of previously published ITS sequences with flanking rDNA coding regions. The specificity of these and other ITS primers used for clitellates were then tested in silico by evaluating their mismatches with all assembled and annotated sequences (STD, version r127) from EMBL, and the new primers were also tested in vitro for a taxonomically broad sample of clitellate species (71 specimens representing 11 families). The in silico analyses showed that the newly designed primers have a better performance than the universal ones when amplifying clitellate ITS sequences. In vitro PCR and sequencing using the new primers were successful, in particular, for the 606F/1082R pair, which worked well for 65 of the 71 specimens. Thus, using this pair for amplifying the ITS2 will facilitate further molecular systematic investigation of various clitellates. The other pair (29F/1084R), will be a useful complement to existing ITS primers, when amplifying ITS as a whole.
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Affiliation(s)
- Yingkui Liu
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
| | - Christer Erséus
- Department of Biological and Environmental Sciences University of Gothenburg Göteborg Sweden
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Zahradníková M, Andersen HL, Tønsberg T, Beck A. Molecular Evidence of Apatococcus, including A. fuscideae sp. nov., as Photobiont in the Genus Fuscidea. Protist 2017; 168:425-438. [PMID: 28803921 DOI: 10.1016/j.protis.2017.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 06/14/2017] [Accepted: 06/19/2017] [Indexed: 01/05/2023]
Abstract
The knowledge of the taxonomy and classification of algae (including lichenized) has recently increased rapidly, but there are still many gaps. We aimed to 1) identify the Fuscidea photobionts by locating their taxonomic positions in the green algal classification, and 2) to resolve their interspecific relationships. The lichenized algae were examined based on morphological observations of axenic isolates as well as molecular studies of 18S and ITS nrDNA sequences. Analysis of the secondary structure of the ITS2 operon complemented these investigations. We found that the Fuscidea photobionts were placed within the Trebouxiophyceae, related to Apatococcus lobatus (Chodat) J.B.Petersen. Phylogenetic analyses revealed one clade nesting free-living and lichenized Apatococcus F.Brand which comprised six different lineages in the ITS phylogeny. The lichenized alga associated with the investigated Fuscidea species, except for F. lightfootii (Sm.) Coppins & James, represents a hitherto unknown lineage within Apatococcus. Fuscidea lightfootii was lichenized with a separate lineage within Apatococcus, together with free-living members, which were already known from Genbank sequences. All retrieved groups within Apatococcus were rather different in their ITS sequences, thus most likely corresponding to different species. The most common photobiont of Fuscidea species, Apatococcus fuscideae A.Beck & Zahradn., was described as new to science.
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Affiliation(s)
- Martina Zahradníková
- Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway.
| | - Heidi L Andersen
- The Arboretum and Botanical Gardens, Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway
| | - Tor Tønsberg
- Department of Natural History, University Museum, University of Bergen, Allégaten 41, P.O. Box 7800, N-5020 Bergen, Norway
| | - Andreas Beck
- Department of Lichenology and Bryology, Botanische Staatssammlung München, 80638 München, Germany
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Kim K, Nguyen VB, Dong J, Wang Y, Park JY, Lee SC, Yang TJ. Evolution of the Araliaceae family inferred from complete chloroplast genomes and 45S nrDNAs of 10 Panax-related species. Sci Rep 2017; 7:4917. [PMID: 28687778 PMCID: PMC5501832 DOI: 10.1038/s41598-017-05218-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/25/2017] [Indexed: 11/09/2022] Open
Abstract
We produced complete sequences and conducted comparative analysis of the maternally inherited chloroplast (cp) genomes and bi-parentally inherited 45S nuclear ribosomal RNA genes (nrDNA) from ten Araliaceae species to elucidate the genetic diversity and evolution in that family. The cp genomes ranged from 155,993 bp to 156,730 bp with 97.1-99.6% similarity. Complete 45S nrDNA units were about 11 kb including a 5.8-kb 45S cistron. Among 79 cp protein-coding genes, 74 showed nucleotide variations among ten species, of which infA, rpl22, rps19 and ndhE genes showed the highest Ks values and atpF, atpE, ycf2 and rps15 genes showed the highest Ka/Ks values. Four genes, petN, psaJ, psbF, and psbN, related to photosynthesis and one gene, rpl23, related to the ribosomal large subunit remain conserved in all 10 Araliaceae species. Phylogenetic analysis revealed that the ten species could be resolved into two monophyletic lineages, the Panax-Aralia and the Eleutherococcus-Dendropanax groups, which diverged approximately 8.81-10.59 million years ago (MYA). The Panax genus divided into two groups, with diploid species including P. notoginseng, P. vietnamensis, and P. japonicus surviving in Southern Asia and a tetraploid group including P. ginseng and P. quinquefolius Northern Asia and North America 2.89-3.20 MYA.
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Affiliation(s)
- Kyunghee Kim
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Van Binh Nguyen
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Jingzhou Dong
- School of Forestry and Horticulture, Hubei University for Nationalities, Enshi, 445000, China
| | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, Guangdong Province, 510650, China
| | - Jee Young Park
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Sang-Choon Lee
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea
| | - Tae-Jin Yang
- Department of Plant Science, Plant Genomics and Breeding Institute, and Research Institute of Agriculture and Life Sciences, College of Agriculture and Life Sciences, Seoul National University, Seoul, 151-921, Republic of Korea. .,Crop Biotechnology Institute/GreenBio Science and Technology, Seoul National University, Pyeongchang, 232-916, Republic of Korea.
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Ghosh JS, Bhattacharya S, Pal A. Molecular phylogeny of 21 tropical bamboo species reconstructed by integrating non-coding internal transcribed spacer (ITS1 and 2) sequences and their consensus secondary structure. Genetica 2017; 145:319-333. [PMID: 28439758 DOI: 10.1007/s10709-017-9967-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 04/20/2017] [Indexed: 11/27/2022]
Abstract
The unavailability of the reproductive structure and unpredictability of vegetative characters for the identification and phylogenetic study of bamboo prompted the application of molecular techniques for greater resolution and consensus. We first employed internal transcribed spacer (ITS1, 5.8S rRNA and ITS2) sequences to construct the phylogenetic tree of 21 tropical bamboo species. While the sequence alone could grossly reconstruct the traditional phylogeny amongst the 21-tropical species studied, some anomalies were encountered that prompted a further refinement of the phylogenetic analyses. Therefore, we integrated the secondary structure of the ITS sequences to derive individual sequence-structure matrix to gain more resolution on the phylogenetic reconstruction. The results showed that ITS sequence-structure is the reliable alternative to the conventional phenotypic method for the identification of bamboo species. The best-fit topology obtained by the sequence-structure based phylogeny over the sole sequence based one underscores closer clustering of all the studied Bambusa species (Sub-tribe Bambusinae), while Melocanna baccifera, which belongs to Sub-Tribe Melocanneae, disjointedly clustered as an out-group within the consensus phylogenetic tree. In this study, we demonstrated the dependability of the combined (ITS sequence+structure-based) approach over the only sequence-based analysis for phylogenetic relationship assessment of bamboo.
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Affiliation(s)
- Jayadri Sekhar Ghosh
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India
- Kentucky Tobacco Research and Development Center, University of Kentucky, Lexington, KY, 40546, USA
| | - Samik Bhattacharya
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Straße 8, 07745, Jena, Germany
| | - Amita Pal
- Division of Plant Biology, Bose Institute, P1/12 CIT Scheme VIIM, Kolkata, 700054, India.
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Nilsson RH, Alm Rosenblad M, Martín MP, Tedersoo L, Ryberg MK, Larsson E, Wurzbacher C, Abarenkov K. Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota). MycoKeys 2016. [DOI: 10.3897/mycokeys.13.8579] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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24
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ITS2 RNA secondary structure analysis reveals close affinity between endophytic and pathogenic fungi: A case study in Fusarium species. ANN MICROBIOL 2015. [DOI: 10.1007/s13213-015-1142-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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