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Jagadeesh D, Prasanna Kumar M, Chandrakanth R, Devaki N. Molecular diversity of internal transcribed spacer among the monoconidial isolates of Magnaporthe oryzae isolated from rice in Southern Karnataka, India. J Genet Eng Biotechnol 2018; 16:631-638. [PMID: 30733782 PMCID: PMC6353761 DOI: 10.1016/j.jgeb.2018.05.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Revised: 04/21/2018] [Accepted: 05/14/2018] [Indexed: 11/20/2022]
Abstract
Blast disease of rice plant is caused by Magnaporthe oryzae (anamorph Pyricularia oryzae). This disease is recognized to be one of the most serious diseases of rice crop around the world. A total of 72 monoconidial isolates of M. oryzae obtained from blast disease samples collected around Southern Karnataka were characterized using internal transcribed spacers of the ribosomal DNA sequences. These were analyzed by comparing with already deposited sequences in GenBank database. It helped in diagnosing the invasive pathogen in all locations. Variability of rDNA sequences was found to be highly polymorphic with 0.068962 nucleotide diversity showing 6 distinct clades. 33 haplotype groups were identified with haplotype diversity of 0.8881 and Tajima's neutrality test with a D value of -1.96827 with P < 0.05 showing the presence of variations among the sequences of pathogen isolates. The Tajima's D value of less than one indicates the presence of a high number of rare alleles. Our study indicates that the pathogen might have undergone recent selection pressure because of the exposure to a large number of cultivars resulting in the evolution of rare alleles. This shows the importance of characterizing internal transcribed spacer (ITS) to know pathogen diversity and its fitness which has potential to contribute to the field of breeding for blast disease resistance.
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Affiliation(s)
- D. Jagadeesh
- Department of Molecular Biology, Yuvaraja’s College, University of Mysore, Mysuru 570005, India
| | - M.K. Prasanna Kumar
- Department of Plant Pathology, GKVK, University of Agricultural Science, Bangalore 560065, India
| | - R. Chandrakanth
- Department of Molecular Biology, Yuvaraja’s College, University of Mysore, Mysuru 570005, India
| | - N.S. Devaki
- Department of Molecular Biology, Yuvaraja’s College, University of Mysore, Mysuru 570005, India
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Du XH, Zhao Q, Yang ZL, Hansen K, Taskin H, Büyükalaca S, Dewsbury D, Moncalvo JM, Douhan GW, Robert VARG, Crous PW, Rehner SA, Rooney AP, Sink S, O'Donnell K. How well do ITS rDNA sequences differentiate species of true morels (Morchella)? Mycologia 2012; 104:1351-68. [PMID: 22802394 DOI: 10.3852/12-056] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Arguably more mycophiles hunt true morels (Morchella) during their brief fruiting season each spring in the northern hemisphere than any other wild edible fungus. Concerns about overharvesting by individual collectors and commercial enterprises make it essential that science-based management practices and conservation policies are developed to ensure the sustainability of commercial harvests and to protect and preserve morel species diversity. Therefore, the primary objectives of the present study were to: (i) investigate the utility of the ITS rDNA locus for identifying Morchella species, using phylogenetic species previously inferred from multilocus DNA sequence data as a reference; and (ii) clarify insufficiently identified sequences and determine whether the named sequences in GenBank were identified correctly. To this end, we generated 553 Morchella ITS rDNA sequences and downloaded 312 additional ones generated by other researchers from GenBank using emerencia and analyzed them phylogenetically. Three major findings emerged: (i) ITS rDNA sequences were useful in identifying 48/62 (77.4%) of the known phylospecies; however, they failed to identify 12 of the 22 species within the species-rich Elata Subclade and two closely related species in the Esculenta Clade; (ii) at least 66% of the named Morchella sequences in GenBank are misidentified; and (iii) ITS rDNA sequences of up to six putatively novel Morchella species were represented in GenBank. Recognizing the need for a dedicated Web-accessible reference database to facilitate the rapid identification of known and novel species, we constructed Morchella MLST (http://www.cbs.knaw.nl/morchella/), which can be queried with ITS rDNA sequences and those of the four other genes used in our prior multilocus molecular systematic studies of this charismatic genus.
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Affiliation(s)
- Xi-Hui Du
- Kunming Institute of Botany, Chinese Academy of Sciences, Yunnan Province, People's Republic of China
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10
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Agüero-Chapín G, González-Díaz H, de la Riva G, Rodríguez E, Sánchez-Rodríguez A, Podda G, Vazquez-Padrón RI. MMM-QSAR Recognition of Ribonucleases without Alignment: Comparison with an HMM Model and Isolation from Schizosaccharomyces pombe, Prediction, and Experimental Assay of a New Sequence. J Chem Inf Model 2008; 48:434-48. [DOI: 10.1021/ci7003225] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guillermín Agüero-Chapín
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Humberto González-Díaz
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Gustavo de la Riva
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Edrey Rodríguez
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Aminael Sánchez-Rodríguez
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Gianni Podda
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
| | - Roberto I. Vazquez-Padrón
- Dipartimento Farmaco Chimico Tecnologico, Universitá Degli Studi di Cagliari, Cagliari, 09124, Italy, CAP, Faculty of Chemistry and Pharmacy, IBP, and CBQ, UCLV, Santa Clara 54830, Cuba, Unit for Bioinformatics & Connectivity Analysis (UBICA), Institute of Industrial Pharmacy and Department of Organic Chemistry, Faculty of Pharmacy, USC, Santiago de Compostela 15782, Spain, CINVESTAV-LANGEBIO, Irapuato, Guanajuato 36821, México, Caribbean Vitroplants, Santo Domingo 1464, Dominican Republic, and Vascular
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Woodhams MD, Stadler PF, Penny D, Collins LJ. RNase MRP and the RNA processing cascade in the eukaryotic ancestor. BMC Evol Biol 2007; 7 Suppl 1:S13. [PMID: 17288571 PMCID: PMC1796607 DOI: 10.1186/1471-2148-7-s1-s13] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Within eukaryotes there is a complex cascade of RNA-based macromolecules that process other RNA molecules, especially mRNA, tRNA and rRNA. An example is RNase MRP processing ribosomal RNA (rRNA) in ribosome biogenesis. One hypothesis is that this complexity was present early in eukaryotic evolution; an alternative is that an initial simpler network later gained complexity by gene duplication in lineages that led to animals, fungi and plants. Recently there has been a rapid increase in support for the complexity-early theory because the vast majority of these RNA-processing reactions are found throughout eukaryotes, and thus were likely to be present in the last common ancestor of living eukaryotes, herein called the Eukaryotic Ancestor. RESULTS We present an overview of the RNA processing cascade in the Eukaryotic Ancestor and investigate in particular, RNase MRP which was previously thought to have evolved later in eukaryotes due to its apparent limited distribution in fungi and animals and plants. Recent publications, as well as our own genomic searches, find previously unknown RNase MRP RNAs, indicating that RNase MRP has a wide distribution in eukaryotes. Combining secondary structure and promoter region analysis of RNAs for RNase MRP, along with analysis of the target substrate (rRNA), allows us to discuss this distribution in the light of eukaryotic evolution. CONCLUSION We conclude that RNase MRP can now be placed in the RNA-processing cascade of the Eukaryotic Ancestor, highlighting the complexity of RNA-processing in early eukaryotes. Promoter analyses of MRP-RNA suggest that regulation of the critical processes of rRNA cleavage can vary, showing that even these key cellular processes (for which we expect high conservation) show some species-specific variability. We present our consensus MRP-RNA secondary structure as a useful model for further searches.
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Affiliation(s)
- Michael D Woodhams
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107, Germany
| | - David Penny
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
| | - Lesley J Collins
- Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand
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