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Sánchez-Flores M, García-Jiménez J, Raymundo T, Martínez-González CR, Hernández-Del Valle JF, Hernández-Muñoz MA, de la Fuente JI, Esqueda M, Ávila Ortiz A, Valenzuela R. Eleven New Species of the Genus Tarzetta (Tarzettaceae, Pezizales) from Mexico. J Fungi (Basel) 2024; 10:403. [PMID: 38921390 PMCID: PMC11204591 DOI: 10.3390/jof10060403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/23/2024] [Accepted: 05/26/2024] [Indexed: 06/27/2024] Open
Abstract
The genus Tarzetta is distributed mainly in temperate forests and establishes ectomycorrhizal associations with angiosperms and gymnosperms. Studies on this genus are scarce in México. A visual, morphological, and molecular (ITS-LSU) description of T. americupularis, T. cupressicola, T. davidii, T. durangensis, T. mesophila, T. mexicana, T. miquihuanensis, T. poblana, T. pseudobronca, T. texcocana, and T. victoriana was carried out in this work, associated with Abies, Quercus, and Pinus. The results of SEM showed an ornamented ascospores formation by Mexican Taxa; furthermore, the results showed that T. catinus and T. cupularis are only distributed in Europe and are not associated with any American host.
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Affiliation(s)
- Marcos Sánchez-Flores
- Herbario Micológico José Castillo Tovar, Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Boulevard Emilio Portes Gil No. 1301, Ciudad Victoria 87010, Tamaulipas, Mexico; (M.S.-F.); (C.R.M.-G.); (J.F.H.-D.V.)
| | - Jesús García-Jiménez
- Herbario Micológico José Castillo Tovar, Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Boulevard Emilio Portes Gil No. 1301, Ciudad Victoria 87010, Tamaulipas, Mexico; (M.S.-F.); (C.R.M.-G.); (J.F.H.-D.V.)
| | - Tania Raymundo
- Laboratorio de Micología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio and Plan de Ayala, Santo Tomás, Alcaldía Miguel Hidalgo, Ciudad de Mexico 11340, Mexico; (T.R.); (R.V.)
| | - César R. Martínez-González
- Herbario Micológico José Castillo Tovar, Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Boulevard Emilio Portes Gil No. 1301, Ciudad Victoria 87010, Tamaulipas, Mexico; (M.S.-F.); (C.R.M.-G.); (J.F.H.-D.V.)
| | - Juan F. Hernández-Del Valle
- Herbario Micológico José Castillo Tovar, Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Boulevard Emilio Portes Gil No. 1301, Ciudad Victoria 87010, Tamaulipas, Mexico; (M.S.-F.); (C.R.M.-G.); (J.F.H.-D.V.)
| | - Marco A. Hernández-Muñoz
- Herbario FEZA, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Batalla de 5 de Mayo s/n, Colonia Ejercito de Oriente, Alcaldía Iztapalapa, Ciudad de Mexico 09230, Mexico; (M.A.H.-M.); (A.Á.O.)
| | - Javier I. de la Fuente
- Edafología, Campus Montecillo, Colegio de Postgraduados, Km 36.5, Montecillo, Texcoco 56230, Estado de México, Mexico;
| | - Martín Esqueda
- Centro de Investigación en Alimentación y Desarrollo A.C., Carretera Gustavo Enrique Astiazarán Rosas 46, La Victoria, Hermosillo 83304, Sonora, Mexico;
| | - Alejandrina Ávila Ortiz
- Herbario FEZA, Facultad de Estudios Superiores Zaragoza, Universidad Nacional Autónoma de México, Batalla de 5 de Mayo s/n, Colonia Ejercito de Oriente, Alcaldía Iztapalapa, Ciudad de Mexico 09230, Mexico; (M.A.H.-M.); (A.Á.O.)
| | - Ricardo Valenzuela
- Laboratorio de Micología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Prolongación de Carpio and Plan de Ayala, Santo Tomás, Alcaldía Miguel Hidalgo, Ciudad de Mexico 11340, Mexico; (T.R.); (R.V.)
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2
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Ramírez-Mendoza R, Ángeles-Argáiz R, Lozano Aguirre-Beltrán LF, Almaraz-Suárez JJ, Hernández-Oaxaca D, Ortiz-Lopez I, Perez-Moreno J. Whole-genome sequence of Pseudomonas yamanorum OLsAu1 isolated from the edible wild ectomycorrhizal mushroom Lactarius sp. section Deliciosi. Microbiol Resour Announc 2023; 12:e0084323. [PMID: 37962344 PMCID: PMC10720402 DOI: 10.1128/mra.00843-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Accepted: 10/03/2023] [Indexed: 11/15/2023] Open
Abstract
We announce the genome sequencing, assembly, and annotation of the OLsAu1 strain and its taxonomic assignment to Pseudomonas yamanorum. The isolate comes from a wild edible ectomycorrhizal Lactarius sp. mushroom in the Abies forest. There is information regarding the strain's ability to promote plant growth, indicating its potential application in forestry.
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Affiliation(s)
| | - Rodolfo Ángeles-Argáiz
- Red de Manejo Biotecnológico de Recursos, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | | | | | - Diana Hernández-Oaxaca
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de Mexico, Cuernavaca, Morelos, Mexico
- Red de Biodiversidad y Sistemática, Instituto de Ecología, Xalapa, Veracruz, Mexico
| | - Ivette Ortiz-Lopez
- Edafología, Campus Montecillo, Colegio de Postgraduados, Texcoco, Estado de Mexico, Mexico
| | - Jesus Perez-Moreno
- Edafología, Campus Montecillo, Colegio de Postgraduados, Texcoco, Estado de Mexico, Mexico
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3
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Romeiro-Brito M, Taylor NP, Zappi DC, Telhe MC, Franco FF, Moraes EM. Unravelling phylogenetic relationships of the tribe Cereeae using target enrichment sequencing. ANNALS OF BOTANY 2023; 132:989-1006. [PMID: 37815357 PMCID: PMC10808018 DOI: 10.1093/aob/mcad153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 10/09/2023] [Indexed: 10/11/2023]
Abstract
BACKGROUND AND AIMS Cactaceae are succulent plants, quasi-endemic to the American continent, and one of the most endangered plant groups in the world. Molecular phylogenies have been key to unravelling phylogenetic relationships among major cactus groups, previously hampered by high levels of morphological convergence. Phylogenetic studies using plastid markers have not provided adequate resolution for determining generic relationships within cactus groups. This is the case for the tribe Cereeae s.l., a highly diverse group from tropical America. Here we aimed to reconstruct a well-resolved phylogenetic tree of tribe Cereeae and update the circumscription of suprageneric and generic groups in this tribe. METHODS We integrated sequence data from public gene and genomic databases with new target sequences (generated using the customized Cactaceae591 probe set) across representatives of this tribe, with a denser taxon sampling of the subtribe Cereinae. We inferred concatenated and coalescent phylogenetic trees and compared the performance of both approaches. KEY RESULTS Six well-supported suprageneric clades were identified using different datasets. However, only genomic datasets, especially the Cactaceae591, were able to resolve the contentious relationships within the subtribe Cereinae. CONCLUSIONS We propose a new taxonomic classification within Cereeae based on well-resolved clades, including new subtribes (Aylosterinae subtr. nov., Uebelmanniinae subtr. nov. and Gymnocalyciinae subtr. nov.) and revised subtribes (Trichocereinae, Rebutiinae and Cereinae). We emphasize the importance of using genomic datasets allied with coalescent inference to investigate evolutionary patterns within the tribe Cereeae.
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Affiliation(s)
- Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Nigel P Taylor
- University of Gibraltar, Gibraltar Botanic Gardens Campus, Gibraltar
| | - Daniela C Zappi
- Programa de Pós-Graduação em Botânica, Instituto de Ciências Biológicas Universidade de Brasília (UNB), Brasília, Distrito Federal, Brazil
| | - Milena C Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Fernando F Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
| | - Evandro M Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba, São Paulo, Brazil
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4
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Ayala-Vásquez O, Martínez-Reyes M, Pérez-Moreno J, Martínez-González CR, Pinzón JP, de la Fuente JI, Castro-Rivera R, García-Jiménez J, Balbuena-Carrasco S, Ramírez-Carbajal E, Yu F. Five New Species of Aureoboletus and Chalciporus (Boletaceae, Boletales) and Their Ethnomycological Aspects. J Fungi (Basel) 2023; 9:1041. [PMID: 37888297 PMCID: PMC10607999 DOI: 10.3390/jof9101041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/14/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023] Open
Abstract
Among Boletales, the family Boletaceae has the highest diversity worldwide. Additionally, this fungal group has great ecological relevance because it not only includes mainly ectomycorrhizal but also saprotrophic species. Furthermore, some species are used as food and have sociocultural and economic importance worldwide. In Mexico, the Boletaceae family boasts a substantial number of species, yet our understanding of these species remains far from comprehensive. In this work, by using macro- and micromorphological and phylogenetic analyses of DNA sequences from multi-gene analyses based on ITS, nrLSU, rpb1, rpb2, and tef1, we report five new species belonging to the genera Aureoboletus and Chalciporus: A. ayuukii and A. elvirae from a Quercus scytophylla forest, A. readii from a mixed forest, C. perezsilvae from cloud forest, and C. piedracanteadensis from both a mixed coniferous forest and a Quercus-Pinus forest. In Mexico, four species of Aureoboletus are used as a food source, and in this work, we add another one, A. readii, which is traditionally consumed by members of the Tlahuica-Pjiekakjoo culture, who are located in the central part of the country. This work contributes to our knowledge of two genera of Boletaceae in a geographical area that is scarcely studied, and thus, our understanding of its biocultural relevance is enriched.
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Affiliation(s)
- Olivia Ayala-Vásquez
- Colegio de Postgraduados, Campus Montecillo, Edafología, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco CP56230, Mexico; (O.A.-V.); (M.M.-R.); (J.I.d.l.F.); (E.R.-C.)
| | - Magdalena Martínez-Reyes
- Colegio de Postgraduados, Campus Montecillo, Edafología, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco CP56230, Mexico; (O.A.-V.); (M.M.-R.); (J.I.d.l.F.); (E.R.-C.)
| | - Jesús Pérez-Moreno
- Colegio de Postgraduados, Campus Montecillo, Edafología, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco CP56230, Mexico; (O.A.-V.); (M.M.-R.); (J.I.d.l.F.); (E.R.-C.)
| | - César Ramiro Martínez-González
- Departamento de Fitotecnia, Instituto de Horticultura, Universidad Autónoma de Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco CP56230, Mexico; (C.R.M.-G.); (S.B.-C.)
| | - Juan Pablo Pinzón
- Departamento de Botánica, Facultad de Medicina Veterinaria y Zootecnia, Universidad Autónoma de Yucatán, Carretera Mérida-Xmatkuil, Km 15.5, Mérida CP97100, Mexico;
| | - Javier Isaac de la Fuente
- Colegio de Postgraduados, Campus Montecillo, Edafología, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco CP56230, Mexico; (O.A.-V.); (M.M.-R.); (J.I.d.l.F.); (E.R.-C.)
| | - Rigoberto Castro-Rivera
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Unidad Tlaxcala, Tepetitla de Lardizábal CP90700, Mexico;
| | - Jesús García-Jiménez
- Tecnológico Nacional de México, Instituto Tecnológico de Ciudad Victoria, Boulevard Emilio Portes Gil #1301Pte, Ciudad Victoria CP87010, Mexico;
| | - Soledad Balbuena-Carrasco
- Departamento de Fitotecnia, Instituto de Horticultura, Universidad Autónoma de Chapingo, Carretera Federal México-Texcoco Km 38.5, Texcoco CP56230, Mexico; (C.R.M.-G.); (S.B.-C.)
| | - Eliseete Ramírez-Carbajal
- Colegio de Postgraduados, Campus Montecillo, Edafología, Carretera México-Texcoco Km. 36.5, Montecillo, Texcoco CP56230, Mexico; (O.A.-V.); (M.M.-R.); (J.I.d.l.F.); (E.R.-C.)
| | - Fuqiang Yu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
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Vásquez C, Leyton-Carcaman B, Cid-Alda FP, Segovia I, Pinto F, Abanto M. Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge. Int J Mol Sci 2023; 24:15243. [PMID: 37894923 PMCID: PMC10607799 DOI: 10.3390/ijms242015243] [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: 08/24/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/29/2023] Open
Abstract
Obtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of specific kits. However, the evaluation of the performance of commercial kits for sludge DNA extraction is scarce and optimization of these methods to obtain a high quantity and quality of DNA is necessary, especially for downstream genomic sequencing. Sequential batch reactors (SBRs) loaded with lignocellulosic biomass are used for the synthesis of renewable resources such as levulinic acid (LA), adipic acid (AA), and polyhydroxyalkanoates (PHAs), and the biochemical synthesis of these compounds is conducted through the inoculation of microbes present in the residual activated sludge (AS) obtained from a municipal wastewater treatment plant. To characterize these microbes, the extraction of DNA from residual sewage sludge was conducted with three different commercial kits: Nucleospin® Soil from Macherey-Nagel, DNEasy® PowerSoil® from Qiagen, and E.Z.N.A.® Plant DNA Kit from Omega BIO-TEK. Nevertheless, to obtain the highest load and quality of DNA for next-generation sequencing (NGS) analysis, different pretreatments and different combinations of these pretreatments were used. The pretreatments considered were an ultrasonic bath and a temperature of 80 °C, together and separately with different incubation time periods of 30, 60, and 90 min. The results obtained suggest a significant improvement in the efficiency and quality of DNA extraction with the three commercial extraction kits when used together with the ultrasonic bath and 80 °C for 60 min. Here, we were able to prove that physical pretreatments are a viable alternative to chemical lysis for DNA extraction from complex samples such as sludge.
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Affiliation(s)
- Claudio Vásquez
- Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile; (C.V.); (B.L.-C.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Benjamín Leyton-Carcaman
- Doctorado en Ciencias Mención Biología Celular y Molecular Aplicada, Universidad de La Frontera, Temuco 4811230, Chile; (C.V.); (B.L.-C.)
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Fernanda P. Cid-Alda
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
| | - Iñaky Segovia
- Carrera de Tecnología Médica, Facultad de Medicina, Universidad de La Frontera, Temuco 4811230, Chile;
| | - Fernanda Pinto
- Departamento de Procesos Industriales, Facultad de Ingeniería, Universidad Católica de Temuco, Casilla 15-D, Temuco 4780000, Chile;
| | - Michel Abanto
- Scientific and Technological Bioresource Nucleus (BIOREN), Universidad de La Frontera, Temuco 4811230, Chile
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Raymundo T, Valenzuela R, Martínez-González CR, García-Jiménez J, Cobos-Villagrán A, Sánchez-Flores M, de la Fuente J, Martínez-Pineda M, Pérez-Valdespino A, Ramírez-Martínez JC, Luna-Vega I. New Ascomycetes from the Mexican Tropical Montane Cloud Forest. J Fungi (Basel) 2023; 9:933. [PMID: 37755041 PMCID: PMC10532444 DOI: 10.3390/jof9090933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/15/2023] [Accepted: 09/01/2023] [Indexed: 09/28/2023] Open
Abstract
The tropical montane cloud forest is the most diverse and threatened vegetation type in Mexico. In the last decade, the number of described Ascomycetes species has notably increased, reaching more than 1300 species. This study describes six new species based on their molecular and morphological characteristics. Our results suggest that Mexico has the highest number of described species in the Neotropics. However, many other Mexican lineages still need to be described.
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Affiliation(s)
- Tania Raymundo
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Botánica, Laboratorio de Micología, Mexico City 11340, Mexico; (T.R.); (R.V.); (A.C.-V.); (M.M.-P.)
| | - Ricardo Valenzuela
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Botánica, Laboratorio de Micología, Mexico City 11340, Mexico; (T.R.); (R.V.); (A.C.-V.); (M.M.-P.)
| | - César Ramiro Martínez-González
- Departamento de Fitotecnia, Instituto de Horticultura, Universidad Autónoma Chapingo, km 38.5 Carretera Federal México-Texcoco, Texcoco 56230, Estado de México, Mexico;
| | - Jesús García-Jiménez
- Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Blvd. Emilio Portes Gil #1301Pte, Ciudad Victoria 87010, Tamaulipas, Mexico; (J.G.-J.); (M.S.-F.)
| | - Aurora Cobos-Villagrán
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Botánica, Laboratorio de Micología, Mexico City 11340, Mexico; (T.R.); (R.V.); (A.C.-V.); (M.M.-P.)
| | - Marcos Sánchez-Flores
- Instituto Tecnológico de Ciudad Victoria, Tecnológico Nacional de México, Blvd. Emilio Portes Gil #1301Pte, Ciudad Victoria 87010, Tamaulipas, Mexico; (J.G.-J.); (M.S.-F.)
| | - Javier de la Fuente
- Colegio de Posgraduados, km 36.5, Montecillo, Texcoco 56230, Estado de México, Mexico;
| | - Michelle Martínez-Pineda
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Botánica, Laboratorio de Micología, Mexico City 11340, Mexico; (T.R.); (R.V.); (A.C.-V.); (M.M.-P.)
| | - Abigail Pérez-Valdespino
- Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Departamento de Bioquímica, Laboratorio de Ingeniería Genética, Mexico City 11340, Mexico;
| | - Julio Cesar Ramírez-Martínez
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
| | - Isolda Luna-Vega
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico;
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7
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Valenzuela R, Luna-Vega I, Martínez-Pineda M, Martínez-González CR, García-Jiménez J, de la Fuente J, Bautista-Hernández S, Acosta-Castellanos S, Raymundo T. Novelties in Macrofungi of the Tropical Montane Cloud Forest in Mexico. J Fungi (Basel) 2023; 9:jof9040477. [PMID: 37108931 PMCID: PMC10143667 DOI: 10.3390/jof9040477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Revised: 04/05/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
The tropical montane cloud forest in Mexico is the most diverse and threatened ecosystem. Mexican macrofungi numbers more than 1408 species. This study described four new species of Agaricomycetes (Bondarzewia, Gymnopilus, Serpula, Sparassis) based on molecular and morphological characteristics. Our results support that Mexico is among the most biodiverse countries in terms of macrofungi in the Neotropics.
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Affiliation(s)
- Ricardo Valenzuela
- Laboratorio de Micología, Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 11340, CDMX, Mexico
| | - Isolda Luna-Vega
- Laboratorio de Biogeografía y Sistemática, Departamento de Biología Evolutiva, Facultad de Ciencias, Universidad Nacional Autónoma de México, Mexico City 04510, CDMX, Mexico
| | - Michelle Martínez-Pineda
- Laboratorio de Micología, Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 11340, CDMX, Mexico
| | - César Ramiro Martínez-González
- Instituto de Horticultura, Departamento de Fitotecnia, Universidad Autónoma Chapingo, Km 38.5 Carretera Federal México-Texcoco, Texcoco 56230, Estado de México, Mexico
| | - Jesús García-Jiménez
- Tecnológico Nacional de México, Instituto Tecnológico de Ciudad Victoria, Blvd. Emilio Portes Gil #1301 Pte., Ciudad Victoria 87010, Tamaulipas, Mexico
| | - Javier de la Fuente
- Colegio de Posgraduados, Km 36.5, Montecillo, Texcoco 56230, Estado de México, Mexico
| | - Silvia Bautista-Hernández
- Laboratorio de Micología, Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 11340, CDMX, Mexico
| | - Salvador Acosta-Castellanos
- Laboratorio de Micología, Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 11340, CDMX, Mexico
| | - Tania Raymundo
- Laboratorio de Micología, Departamento de Botánica, Instituto Politécnico Nacional, Escuela Nacional de Ciencias Biológicas, Mexico City 11340, CDMX, Mexico
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8
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de la Fuente JI, García-Jiménez J, Raymundo T, Sánchez-Flores M, Valenzuela R, Guevara-Guerrero G, Pérez-Ovando EC, Martínez-González CR. Elaphomyces castilloi (Elaphomycetaceae, Ascomycota) and Entoloma secotioides (Entolomataceae, Basidiomycota), two new sequestrate fungi from tropical montane cloud forest from south Mexico. MycoKeys 2023; 96:127-142. [DOI: 10.3897/mycokeys.96.98320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/15/2023] [Indexed: 04/05/2023] Open
Abstract
Two new species of sequestrate fungi are described from south Mexico based on morphological and molecular evidences. Here we describe Elaphomyces castilloi characterized by the yellowish mycelial mat, dull blue gleba and ascospores of 9.7–11.5 µm; Entoloma secotioides is characterized by the secotioid basidiomata, sulcate, pale cream pileus, and basidiospores of 7–13 × 5–9 µm. Both species grow in montane cloud forest under Quercus sp. in the state of Chiapas, Mexico. Descriptions, photographs, and multilocus phylogeny for both species are presented.
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Rache-Cardenal LY, Albesiano-Hoyos AS, Tall H. Optimization of a DNA extraction method using Subepidermis from Austrocylindropuntia and Opuntia-Opuntioideae. REVISTA DE INVESTIGACIÓN, DESARROLLO E INNOVACIÓN 2022. [DOI: 10.19053/20278306.v12.n2.2022.15273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The taxonomic identification of species through analysis of the variation of orthologous DNA sequences, complement the information obtained with morphological characters. Cytogenetic studies indicate that polyploid taxa occur in the subfamily Opuntioideae, Opuntia ficus-indica, contributing to morphological variability in the individuals of a population, and influencing the correct identification of species. However, the lengths of the sequences in Opuntioideae are affected by the extraction of pure DNA. Different extraction methods were evaluated and modified, and a procedure was established to obtain good quality DNA, free of inhibitors for gene amplification by polymerase chain reaction. The ratio A260/A280 and A260/A230 ranged from 1.6 to 2.1, revealing absence of contamination with the modified protocol for DNA extraction from cotton leaves. This method is inexpensive compared to those of commercial manufacturers and, therefore, can be applied in studies with limited resources.
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Franco FF, Amaral DT, Bonatelli IAS, Romeiro-Brito M, Telhe MC, Moraes EM. Evolutionary Genetics of Cacti: Research Biases, Advances and Prospects. Genes (Basel) 2022; 13:452. [PMID: 35328006 PMCID: PMC8952820 DOI: 10.3390/genes13030452] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/22/2022] [Accepted: 02/25/2022] [Indexed: 02/01/2023] Open
Abstract
Here, we present a review of the studies of evolutionary genetics (phylogenetics, population genetics, and phylogeography) using genetic data as well as genome scale assemblies in Cactaceae (Caryophyllales, Angiosperms), a major lineage of succulent plants with astonishing diversity on the American continent. To this end, we performed a literature survey (1992-2021) to obtain detailed information regarding key aspects of studies investigating cactus evolution. Specifically, we summarize the advances in the following aspects: molecular markers, species delimitation, phylogenetics, hybridization, biogeography, and genome assemblies. In brief, we observed substantial growth in the studies conducted with molecular markers in the past two decades. However, we found biases in taxonomic/geographic sampling and the use of traditional markers and statistical approaches. We discuss some methodological and social challenges for engaging the cactus community in genomic research. We also stressed the importance of integrative approaches, coalescent methods, and international collaboration to advance the understanding of cactus evolution.
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Affiliation(s)
- Fernando Faria Franco
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Danilo Trabuco Amaral
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
- Programa de Pós-graduação em Biologia Comparada, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo (USP), Ribeirão Preto 14040-901, Brazil
| | - Isabel A. S. Bonatelli
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo 04021-001, Brazil;
| | - Monique Romeiro-Brito
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Milena Cardoso Telhe
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
| | - Evandro Marsola Moraes
- Departamento de Biologia, Centro de Ciências Humanas e Biológicas, Universidade Federal de São Carlos (UFSCar), Sorocaba 18052-780, Brazil; (F.F.F.); (D.T.A.); (M.R.-B.); (M.C.T.)
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11
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Fiore MC, Marchese A, Mauceri A, Digangi I, Scialabba A. Diversity Assessment and DNA-Based Fingerprinting of Sicilian Hazelnut ( Corylus avellana L.) Germplasm. PLANTS (BASEL, SWITZERLAND) 2022; 11:631. [PMID: 35270101 PMCID: PMC8912283 DOI: 10.3390/plants11050631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/23/2022] [Accepted: 02/23/2022] [Indexed: 11/16/2022]
Abstract
The characterization of plant genetic resources is a precondition for genetic improvement and germplasm management. The increasing use of molecular markers for DNA-based genotype signature is crucial for variety identification and traceability in the food supply chain. We collected 75 Sicilian hazelnut accessions from private and public field collections, including widely grown varieties from the Nebrodi Mountains in north east Sicily (Italy). The germplasm was fingerprinted through nine standardized microsatellites (SSR) for hazelnut identification to evaluate the genetic diversity of the collected accessions, validating SSR discrimination power. We identified cases of homonymy and synonymy among acquisitions and the unique profiles. The genetic relationships illustrated by hierarchical clustering, structure, and discriminant analyses revealed a clear distinction between local and commercial varieties. The comparative genetic analysis also showed that the Nebrodi genotypes are significantly different from the Northern Italian, Iberian, and Turkish genotypes. These results highlight the need and urgency to preserve Nebrodi germplasm as a useful and valuable source for traits of interest employable for breeding. Our study demonstrates the usefulness of molecular marker analysis to select a reference germplasm collection of Sicilian hazelnut varieties and to implement certified plants' production in the supply chain.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics—Research Centre for Plant Protection and Certification, S.S. 113 km 245,500, 90011 Bagheria, Italy
| | - Annalisa Marchese
- Department of Agricultural, Food and Forest Sciences, University of Palermo, Viale delle Scienze—Ed. 4, 90128 Palermo, Italy;
| | - Antonio Mauceri
- Department Agraria, University Mediterranea of Reggio Calabria, Loc. Feo di Vito snc, 89065 Reggio Calabria, Italy;
| | - Ignazio Digangi
- Living Plants Germplasm Bank of Nebrodi, Contrada Pirato, 98060 Ucria, Italy;
| | - Anna Scialabba
- Department of Biological, Chemical and Pharmaceutical Science and Technologies (STEBICEF), University of Palermo, Via Archirafi 38, 90123 Palermo, Italy;
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12
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Vilanova S, Alonso D, Gramazio P, Plazas M, García-Fortea E, Ferrante P, Schmidt M, Díez MJ, Usadel B, Giuliano G, Prohens J. SILEX: a fast and inexpensive high-quality DNA extraction method suitable for multiple sequencing platforms and recalcitrant plant species. PLANT METHODS 2020; 16:110. [PMID: 32793297 PMCID: PMC7419208 DOI: 10.1186/s13007-020-00652-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 08/03/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND The use of sequencing and genotyping platforms has undergone dramatic improvements, enabling the generation of a wealth of genomic information. Despite this progress, the availability of high-quality genomic DNA (gDNA) in sufficient concentrations is often a main limitation, especially for third-generation sequencing platforms. A variety of DNA extraction methods and commercial kits are available. However, many of these are costly and frequently give either low yield or low-quality DNA, inappropriate for next generation sequencing (NGS) platforms. Here, we describe a fast and inexpensive DNA extraction method (SILEX) applicable to a wide range of plant species and tissues. RESULTS SILEX is a high-throughput DNA extraction protocol, based on the standard CTAB method with a DNA silica matrix recovery, which allows obtaining NGS-quality high molecular weight genomic plant DNA free of inhibitory compounds. SILEX was compared with a standard CTAB extraction protocol and a common commercial extraction kit in a variety of species, including recalcitrant ones, from different families. In comparison with the other methods, SILEX yielded DNA in higher concentrations and of higher quality. Manual extraction of 48 samples can be done in 96 min by one person at a cost of 0.12 €/sample of reagents and consumables. Hundreds of tomato gDNA samples obtained with either SILEX or the commercial kit were successfully genotyped with Single Primer Enrichment Technology (SPET) with the Illumina HiSeq 2500 platform. Furthermore, DNA extracted from Solanum elaeagnifolium using this protocol was assessed by Pulsed-field gel electrophoresis (PFGE), obtaining a suitable size ranges for most sequencing platforms that required high-molecular-weight DNA such as Nanopore or PacBio. CONCLUSIONS A high-throughput, fast and inexpensive DNA extraction protocol was developed and validated for a wide variety of plants and tissues. SILEX offers an easy, scalable, efficient and inexpensive way to extract DNA for various next-generation sequencing applications including SPET and Nanopore among others.
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Affiliation(s)
- Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - David Alonso
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Pietro Gramazio
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, 305-8572 Tsukuba, Japan
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Edgar García-Fortea
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Paola Ferrante
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | | | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Björn Usadel
- BG-4 Bioinformatics, Forschungszentrum Jülich, 52428 Jülich, Germany
- CEPLAS, Institute for Biological Data Science, Heinrich Heine University Düsseldorf, 40225 Düsselforf, Germany
| | - Giovanni Giuliano
- ENEA, Italian National Agency for New Technologies, Energy and Sustainable Economic Development, Rome, Italy
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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Peña-Ramírez R, Ge ZW, Gaitán-Hernández R, Martínez-González CR, Guevara-Guerrero G. A novel sequestrate species from Mexico: Aroramyces guanajuatensis sp. nov. (Hysterangiaceae, Hysterangiales). MycoKeys 2019; 61:27-37. [PMID: 31866740 PMCID: PMC6920220 DOI: 10.3897/mycokeys.61.36444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/16/2019] [Indexed: 11/12/2022] Open
Abstract
Knowledge of sequestrate Hysterangiaceae fungi in Mexico is very limited. In the present study, a new member of the family, Aroramyces guanajuatensis sp. nov., is described. This speciesis closely related to A. balanosporus, but differs from the latter in possessing a tomentose peridium 165-240 µm thick, with occasional large terminal hyphae up to 170 µm, a variable mesocutis (isodiametric to angular), and distinct bright yellowish subcutis. In contrast, A. balanosporus possesses a fibrillose peridial surface with shorter hyphae, a peridium 200-450 µm thick, and a mainly hyaline isodiametric mesocutis with a slightly wider subcutis. The phylogenetic analysis of the LSU gene separated A. guanajuatensis from A. balanosporus with a Bayesian posterior probability (PP) = 1. This is the third Aroramyces species described for the American continent.
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Affiliation(s)
- Rafael Peña-Ramírez
- Instituto Tecnológico de Cd. Victoria, Av. Portes Gil 1301 Pte. C.P. 87010, Cd. Victoria Tam, Mexico.,Kunming Institute of Botany, Chinese Academy of Sciences, 132, Lanhei Road, Kunming 650201, China
| | - Zai-Wei Ge
- Kunming Institute of Botany, Chinese Academy of Sciences, 132, Lanhei Road, Kunming 650201, China
| | - Rigoberto Gaitán-Hernández
- Universidad Nacional Autónoma de México, Profesor de Asignatura B, Departamento de Biología, Facultad de Ciencias Ciudad Universitaria, Delegación Coyoacán, 04510, Ciudad de México, Mexico
| | - César Ramiro Martínez-González
- Instituto Tecnológico de Cd. Victoria, Av. Portes Gil 1301 Pte. C.P. 87010, Cd. Victoria Tam, Mexico.,Kunming Institute of Botany, Chinese Academy of Sciences, 132, Lanhei Road, Kunming 650201, China.,Instituto de Ecología, A.C., Carretera antigua a Coatepec # 351, El Haya, C.P. 91070, Xalapa, Veracruz, Mexico.,Universidad Nacional Autónoma de México, Profesor de Asignatura B, Departamento de Biología, Facultad de Ciencias Ciudad Universitaria, Delegación Coyoacán, 04510, Ciudad de México, Mexico
| | - Gonzalo Guevara-Guerrero
- Instituto Tecnológico de Cd. Victoria, Av. Portes Gil 1301 Pte. C.P. 87010, Cd. Victoria Tam, Mexico
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A simple and effective method to obtain high DNA quality and quantity from Cerrado plant species. Mol Biol Rep 2019; 46:4611-4615. [PMID: 31073915 DOI: 10.1007/s11033-019-04845-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 04/30/2019] [Indexed: 02/03/2023]
Abstract
Despite the importance in conservation and breeding purposes, molecular studies using Cerrado plant species are still rare, mainly because of their high amounts of secondary compounds, impeding DNA extraction to downstream applications, such as PCR amplification. To date, the DNA extraction methods described are sometimes inadequate for these species, expensive, time-intensive and/or use very toxic reagents. Here, we present a simple and effective method, based on SDS and Triton X-100, to obtain high DNA quality and quantity from Cerrado plant species for molecular biological techniques. The DNA obtained by our protocol was free of contaminants and excellent for enzymatic restriction and PCR amplification. The concentration of extracted DNA across all tested species ranged from 156 to 1166 ng µL-1 (1.56-11.66 µg g-1 of dry tissue), with an A260/A280 ratio from 1.78 to 1.92. The new DNA extraction protocol described here provides high DNA quality and quantity from Cerrado plant species in a fast, simple and less toxic way. Thus, the use of our method will allow ecologists, geneticists and breeders to rapidly obtain high-quality and -quantity DNA from Cerrado plant species for any molecular biology study.
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Johnson G. High throughput DNA extraction of legume root nodules for rhizobial metagenomics. AMB Express 2019; 9:47. [PMID: 30969386 PMCID: PMC6458200 DOI: 10.1186/s13568-019-0771-z] [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: 11/07/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022] Open
Abstract
A novel combination of tissue homogenization, cell lysis, and DNA purification techniques was developed for isolating total DNA from whole legume root nodules on an automated robotic system. Silica dehydrated root nodules from soy bean, Glycine max cv. Tara, and mung bean, Vigna radiata cv. Crystal, were homogenized in 96-well plates and were enzymatically and chemically lysed before being loaded into the AutoGenprep 965 for automated phenol–chloroform based DNA isolation. The resulting DNAs were of relatively high concentration, low fragmentation, and free of phenolic and polysaccharide contaminants. In contrast to manual methods, this adaptation of the Autogen Prep automated DNA extraction instrument allows for 100’s to 1000’s of samples to be prepared in a fraction of the time and cost.
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Marengo A, Cagliero C, Sgorbini B, Anderson JL, Emaus MN, Bicchi C, Bertea CM, Rubiolo P. Development of an innovative and sustainable one-step method for rapid plant DNA isolation for targeted PCR using magnetic ionic liquids. PLANT METHODS 2019; 15:23. [PMID: 30899320 PMCID: PMC6408755 DOI: 10.1186/s13007-019-0408-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/02/2019] [Indexed: 06/01/2023]
Abstract
BACKGROUND Nowadays, there is an increasing demand for fast and reliable plant biomolecular analyses. Conventional methods for the isolation of nucleic acids are time-consuming and require multiple and often non-automatable steps to remove cellular interferences, with consequence that sample preparation is the major bottleneck in the bioanalytical workflow. New opportunities have been created by the use of magnetic ionic liquids (MILs) thanks to their affinity for nucleic acids. RESULTS In the present study, a MIL-based magnet-assisted dispersive liquid-liquid microextraction (maDLLME) method was optimized for the extraction of genomic DNA from Arabidopsis thaliana (L.) Heynh leaves. MILs containing different metal centers were tested and the extraction method was optimized in terms of MIL volume and extraction time for purified DNA and crude lysates. The proposed approach yielded good extraction efficiency and is compatible with both quantitative analysis through fluorimetric-based detection and qualitative analysis as PCR amplification of multi and single locus genes. The protocol was successfully applied to a set of plant species and tissues. CONCLUSIONS The developed MIL-based maDLLME approach exhibits good enrichment of nucleic acids for extraction of template suitable for targeted PCR; it is very fast, sustainable and potentially automatable thereby representing a powerful tool for screening plants rapidly using DNA-based methods.
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Affiliation(s)
- Arianna Marengo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cecilia Cagliero
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Barbara Sgorbini
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | | | - Miranda N. Emaus
- Department of Chemistry, Iowa State University, Ames, IA 50011 USA
| | - Carlo Bicchi
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
| | - Cinzia M. Bertea
- Dipartimento di Scienze della Vita e Biologia dei Sistemi, Unità di Fisiologia Vegetale, Università di Torino, via Quarello 15/A, 10135 Turin, Italy
| | - Patrizia Rubiolo
- Dipartimento di Scienza e Tecnologia del Farmaco, Università di Torino, Via P. Giuria 9, 10125 Turin, Italy
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