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da Silva AS, Rennó MHL, Quitania ACR, Café-Filho AC, Miller RNG, de Araújo AE, Pinho DB. Ramularia leaf spot: PCR-based methods reveal widespread distribution of Ramulariopsis pseudoglycines and limited presence of R. gossypii in Brazil. Sci Rep 2023; 13:9826. [PMID: 37330533 PMCID: PMC10276850 DOI: 10.1038/s41598-023-33530-3] [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: 03/17/2022] [Accepted: 04/14/2023] [Indexed: 06/19/2023] Open
Abstract
Whilst Brazil is the fourth largest cotton producer globally, incidence of ramularia leaf spot (RLS) has decreased yield. In 2017-18 and 2018-19, ca. 300 fungal samples were collected throughout Brazil. Hyphal tip cultures were obtained for amplification of the RNA polymerase II (RPB2), 28S rRNA, the ribosomal DNA internal transcribed spacers (ITS), actin (ACT), elongation factor (EF1-α) and histone H3 (HIS3) genomic regions. Additionally, sequences of the glyceraldehyde-3-phosphate dehydrogenase (GAPDH) were obtained by nanopore sequencing and the EF1-α region was selected as a marker for rapid recognition of Ramulariopsis species. Clade assignments based on the concatenated-sequence tree were identical to those in tree generated by RPB2-sequences, as well as in an RPB2 haplotype network and an ISSR (TGTC)4 dendrogram, in identification with species-specific primers and based on morphological comparisons. Out of 267 examined isolates, 252 were identified as Ramulariopsis pseudoglycines, indicating this species as the most widespread causal agent of cotton RLS in the Brazilian growing regions. Species-specific primers developed in the study that target the EF1-α gene provide an opportunity for extensive RLS sampling worldwide to study the distribution of Ramulariopsis species. Such data will aid breeders and plant pathologists in cotton disease resistance development and fungicide resistance avoidance.
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da Silva Ribeiro A, Polonio JC, Dos Santos Oliveira JA, Ferreira AP, Alves LH, Mateus NJ, Mangolin CA, de Azevedo JL, Pamphile JA. Retrotransposons and multilocus sequence analysis reveals diversity and genetic variability in endophytic fungi-associated with Serjania laruotteana Cambess. Braz J Microbiol 2021; 52:2179-2192. [PMID: 34491570 DOI: 10.1007/s42770-021-00605-0] [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: 11/21/2020] [Accepted: 08/30/2021] [Indexed: 11/28/2022] Open
Abstract
The composition of endophytic communities is dynamic and demonstrates host specificity; besides, they have great intra- and interspecific genetic variability. In this work, we isolated leaf endophytic fungi from Serjania laruotteana, identify them using multilocus analysis, and evaluate the genetic variability using IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microssatellite amplified polymorphism). A total of 261 fungi were isolated and 58 were identified. Multilocus phylogenetic analysis using the partial sequences from the ITS1-5.8S-ITS2 regions, elongation factor 1-alpha, β-tubulin, actin, glyceraldehyde-3-phosphate dehydrogenase, and calmodulin genes identify that most strains belonged to the Colletotrichum and Diaporthe genera, other isolated genera were Xylaria, Phyllosticta, Muyocopron, Fusarium, Nemania, Plectosphaerella, Corynespora, Bipolaris, and Curvularia. The IRAP and REMAP analyzes were performed with Colletotrichum and Diaporthe genera and showed 100% of polymorphism and high intra- and interspecific variability. This is the first report of the diversity of endophytic fungi from S. laruotteana. In addition, it demonstrated that the IRAP and REMAP can be used to distinguish morphologically similar lineages, revealing differences even strains of the same species.
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Affiliation(s)
- Amanda da Silva Ribeiro
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - Julio Cesar Polonio
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil.
| | - João Arthur Dos Santos Oliveira
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - Ana Paula Ferreira
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - Leonardo Hamamura Alves
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - Natieli Jenifer Mateus
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - Claudete Aparecida Mangolin
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
| | - João Lúcio de Azevedo
- Department of Genetics, Escola Superior de Agricultura Luiz de Queiroz (ESALQ/USP), Piracicaba, São Paulo, 13418-900, Brazil
| | - João Alencar Pamphile
- Department of Biotechnology, Genetics and Cell Biology, Universidade Estadual de Maringá, Avenida Colombo, 5790, Maringa, Paraná, 87020-900, Brazil
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Šatović E, Luchetti A, Pasantes JJ, García-Souto D, Cedilak A, Mantovani B, Plohl M. Terminal-Repeat Retrotransposons in Miniature (TRIMs) in bivalves. Sci Rep 2019; 9:19962. [PMID: 31882746 PMCID: PMC6934838 DOI: 10.1038/s41598-019-56502-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 12/13/2019] [Indexed: 12/12/2022] Open
Abstract
Terminal repeat retrotransposons in miniature (TRIMs) are small non-autonomous LTR retrotransposons consisting of two terminal direct repeats surrounding a short internal domain. The detection and characterization of these elements has been mainly limited to plants. Here we present the first finding of a TRIM element in bivalves, and among the first known in the kingdom Animalia. Class Bivalvia has high ecological and commercial importance in marine ecosystems and aquaculture, and, in recent years, an increasing number of genomic studies has addressed to these organisms. We have identified biv-TRIM in several bivalve species: Donax trunculus, Ruditapes decussatus, R. philippinarum, Venerupis corrugata, Polititapes rhomboides, Venus verrucosa, Dosinia exoleta, Glycymeris glycymeris, Cerastoderma edule, Magallana gigas, Mytilus galloprovincialis. biv-TRIM has several characteristics typical for this group of elements, exhibiting different variations. In addition to canonically structured elements, solo-TDRs and tandem repeats were detected. The presence of this element in the genome of each species is <1%. The phylogenetic analysis showed a complex clustering pattern of biv-TRIM elements, and indicates the involvement of horizontal transfer in the spreading of this element.
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Affiliation(s)
- Eva Šatović
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia.
| | - Andrea Luchetti
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Juan J Pasantes
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, Vigo, Spain
| | - Daniel García-Souto
- Departamento de Bioquímica, Xenética e Inmunoloxía, Universidade de Vigo, Vigo, Spain
- Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Cancer, Ageing and Somatic Mutation, Wellcome Sanger Institute, Hinxton, Cambridgeshire, CB10 1SA, UK
| | - Andrea Cedilak
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
| | - Barbara Mantovani
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, Università di Bologna, Bologna, Italy
| | - Miroslav Plohl
- Division of Molecular Biology, Ruđer Bošković Institute, Zagreb, Croatia
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Zhang L, Yan L, Jiang J, Wang Y, Jiang Y, Yan T, Cao Y. The structure and retrotransposition mechanism of LTR-retrotransposons in the asexual yeast Candida albicans. Virulence 2014; 5:655-64. [PMID: 25101670 PMCID: PMC4139406 DOI: 10.4161/viru.32180] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Retrotransposons constitute a major part of the genome in a number of eukaryotes. Long-terminal repeat (LTR) retrotransposons are one type of the retrotransposons. Candida albicans have 34 distinct LTR-retrotransposon families. They respectively belong to the Ty1/copia and Ty3/gypsy groups which have been extensively studied in the model yeast Saccharomyces cerevisiae. LTR-retrotransposons carry two LTRs flanking a long internal protein-coding domain, open reading frames. LTR-retrotransposons use RNA as intermediate to synthesize double-stranded DNA copies. In this article, we describe the structure feature, retrotransposition mechanism and the influence on organism diversity of LTR retrotransposons in C. albicans. We also discuss the relationship between pathogenicity and LTR retrotransposons in C. albicans.
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Affiliation(s)
- Lulu Zhang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Lan Yan
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Jingchen Jiang
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Yan Wang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Yuanying Jiang
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
| | - Tianhua Yan
- Department of Pharmacology; School of Pharmacy; China Pharmaceutical University; Nanjing, PR China
| | - Yongbing Cao
- Research and Develop Center of New Drug; School of Pharmacy; Second Military Medical University; Shanghai, PR China
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