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Inhibition of platelet aggregation by extracts and compounds from the leaves of Chilean bean landraces (Phaseolus vulgaris L.). J Funct Foods 2023. [DOI: 10.1016/j.jff.2022.105388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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2
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Aguilar OM, Collavino MM, Mancini U. Nodulation competitiveness and diversification of symbiosis genes in common beans from the American centers of domestication. Sci Rep 2022; 12:4591. [PMID: 35301409 PMCID: PMC8931114 DOI: 10.1038/s41598-022-08720-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 02/24/2022] [Indexed: 11/09/2022] Open
Abstract
Phaseolus vulgaris (common bean), having a proposed Mexican origin within the Americas, comprises three centers of diversification: Mesoamerica, the southern Andes, and the Amotape-Huancabamba Depression in Peru-Ecuador. Rhizobium etli is the predominant rhizobium found symbiotically associated with beans in the Americasalthough closely related Rhizobium phylotypes have also been detected. To investigate if symbiosis between bean varieties and rhizobia evolved affinity, firstly nodulation competitiveness was studied after inoculation with a mixture of sympatric and allopatric rhizobial strains isolated from the respective geographical regions. Rhizobia strains harboring nodC types α and \documentclass[12pt]{minimal}
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\begin{document}$$\upgamma$$\end{document}γ, which were found predominant in Mexico and Ecuador, were comparable in nodule occupancy at 50% of each in beans from the Mesoamerican and Andean gene pools, but it is one of those two nodC types which clearly predominated in Ecuadorian-Peruvian beans as well as in Andean beans nodC type \documentclass[12pt]{minimal}
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\begin{document}$$\upgamma$$\end{document}γ predominated the sympatric nodC type δ. The results indicated that those beans from Ecuador-Peru and Andean region, respectively exhibited no affinity for nodulation by the sympatric rhizobial lineages that were found to be predominant in bean nodules formed in those respective areas. Unlike the strains isolated from Ecuador, Rhizobium etli isolated from Mexico as well from the southern Andes was highly competitive for nodulation in beans from Ecuador-Peru, and quite similarly competitive in Mesoamerican and Andean beans. Finally, five gene products associated with symbiosis were examined to analyze variations that could be correlated with nodulation competitiveness. A small GTPase RabA2, transcriptional factors NIN and ASTRAY, and nodulation factor receptors NFR1 and NFR5- indicated high conservation but NIN, NFR1 and NFR5 of beans representative of the Ecuador-Peru genetic pool clustered separated from the Mesoamerican and Andean showing diversification and possible different interaction. These results indicated that both host and bacterial genetics are important for mutual affinity, and that symbiosis is another trait of legumes that could be sensitive to evolutionary influences and local adaptation.
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Affiliation(s)
- O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina.
| | - Mónica M Collavino
- Instituto de Botánica del Nordeste (IBONE), Facultad de Ciencias Agrarias, Universidad Nacional del Nordeste-CONICET, Corrientes, Argentina
| | - Ulises Mancini
- Instituto de Biotecnología y Biología Molecular (IBBM), Universidad Nacional de La Plata-CONICET, La Plata, Argentina
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Martínez-Romero E, Aguirre-Noyola JL, Taco-Taype N, Martínez-Romero J, Zuñiga-Dávila D. Plant microbiota modified by plant domestication. Syst Appl Microbiol 2020; 43:126106. [PMID: 32847781 DOI: 10.1016/j.syapm.2020.126106] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/19/2020] [Accepted: 06/20/2020] [Indexed: 12/19/2022]
Abstract
Human life became largely dependent on agricultural products after distinct crop-domestication events occurred around 10,000 years ago in different geographical sites. Domestication selected suitable plants for human agricultural practices with unexpected consequences on plant microbiota, which has notable effects on plant growth and health. Among other traits, domestication has changed root architecture, exudation, or defense responses that could have modified plant microbiota. Here we present the comparison of reported data on the microbiota from widely consumed cereals and legumes and their ancestors showing that different bacteria were found in domesticated and wild plant microbiomes in some cases. Considering the large variability in plant microbiota, adequate sampling efforts and function-based approaches are needed to further support differences between the microbiota from wild and domesticated plants. The study of wild plant microbiomes could provide a valuable resource of unexploited beneficial bacteria for crops.
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Affiliation(s)
| | | | - Nataly Taco-Taype
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
| | | | - Doris Zuñiga-Dávila
- Laboratorio de Ecología Microbiana, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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4
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Rocha G, Le Queré A, Medina A, Cuéllar A, Contreras JL, Carreño R, Bustillos R, Muñoz-Rojas J, Villegas MDC, Chaintreuil C, Dreyfus B, Munive JA. Diversity and phenotypic analyses of salt- and heat-tolerant wild bean Phaseolus filiformis rhizobia native of a sand beach in Baja California and description of Ensifer aridi sp. nov. Arch Microbiol 2019; 202:309-322. [PMID: 31659382 PMCID: PMC7012998 DOI: 10.1007/s00203-019-01744-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Revised: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 11/30/2022]
Abstract
In northern Mexico, aridity, salinity and high temperatures limit areas that can be cultivated. To investigate the nature of nitrogen-fixing symbionts of Phaseolus filiformis, an adapted wild bean species native to this region, their phylogenies were inferred by MLSA. Most rhizobia recovered belong to the proposed new species Ensifer aridi. Phylogenetic analyses of nodC and nifH show that Mexican isolates carry symbiotic genes acquired through horizontal gene transfer that are divergent from those previously characterized among bean symbionts. These strains are salt tolerant, able to grow in alkaline conditions, high temperatures, and capable of utilizing a wide range of carbohydrates and organic acids as carbon sources for growth. This study improves the knowledge on diversity, geographic distribution and evolution of bean-nodulating rhizobia in Mexico and further enlarges the spectrum of microsymbiont with which Phaseolus species can interact with, including cultivated bean varieties, notably under stressed environments. Here, the species Ensifer aridi sp. nov. is proposed as strain type of the Moroccan isolate LMR001T (= LMG 31426T; = HAMBI 3707T) recovered from desert sand dune.
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Affiliation(s)
- Guadalupe Rocha
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Antoine Le Queré
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - Arturo Medina
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Alma Cuéllar
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - José-Luis Contreras
- Facultad de Arquitectura, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Ricardo Carreño
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Rocío Bustillos
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - Jesús Muñoz-Rojas
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico
| | - María Del Carmen Villegas
- Helyx Affaires SC, Rumania 923-2. Col. Portales-Sur. Alcaldía Benito Juárez, CP-03300, Cd. de México, Mexico
| | - Clémence Chaintreuil
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - Bernard Dreyfus
- IRD/CIRAD/UM2/Supagro-UR 040 Laboratoire des Symbioses Tropicales et Méditerranéennes, 34398, Montpellier, France
| | - José-Antonio Munive
- Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Av. San Claudio S/N, CP-72570, Puebla, Mexico.
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Ormeño-Orrillo E, Martínez-Romero E. A Genomotaxonomy View of the Bradyrhizobium Genus. Front Microbiol 2019; 10:1334. [PMID: 31263459 PMCID: PMC6585233 DOI: 10.3389/fmicb.2019.01334] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 05/28/2019] [Indexed: 11/13/2022] Open
Abstract
Whole genome analysis of the Bradyrhizobium genus using average nucleotide identity (ANI) and phylogenomics showed the genus to be essentially monophyletic with seven robust groups within this taxon that includes nitrogen-fixing nodule forming bacteria as well as free living strains. Despite the wide genetic diversity of these bacteria no indication was found to suggest that the Bradyrhizobium genus have to split in different taxa. Bradyrhizobia have larger genomes than other genera of the Bradyrhizobiaceae family, probably reflecting their metabolic diversity and different lifestyles. Few plasmids in the sequenced strains were revealed from rep gene analysis and a relatively low proportion of the genome is devoted to mobile genetic elements. Sequence diversity of recA and glnII gene metadata was used to theoretically estimate the number of existing species and to predict how many would exist. There may be many more species than those presently described with predictions of around 800 species in nature. Different arguments are presented suggesting that nodulation might have arose in the ancestral genus Bradyrhizobium.
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Affiliation(s)
- Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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Ramírez-Puebla ST, Hernández MAR, Guerrero Ruiz G, Ormeño-Orrillo E, Martinez-Romero JC, Servín-Garcidueñas LE, Núñez-de la Mora A, Amescua-Villela G, Negrete-Yankelevich S, Martínez-Romero E. Nodule bacteria from the cultured legume Phaseolus dumosus (belonging to the Phaseolus vulgaris cross-inoculation group) with common tropici phenotypic characteristics and symbiovar but distinctive phylogenomic position and chromid. Syst Appl Microbiol 2018; 42:373-382. [PMID: 30612723 DOI: 10.1016/j.syapm.2018.12.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/15/2018] [Accepted: 12/16/2018] [Indexed: 10/27/2022]
Abstract
Phaseolus dumosus is an endemic species from mountain tops in Mexico that was found in traditional agriculture areas in Veracruz, Mexico. P. dumosus plants were identified by ITS sequences and their nodules were collected from agricultural fields or from trap plant experiments in the laboratory. Bacteria from P. dumosus nodules were identified as belonging to the phaseoli-etli-leguminosarum (PEL) or to the tropici group by 16S rRNA gene sequences. We obtained complete closed genomes from two P. dumosus isolates CCGE531 and CCGE532 that were phylogenetically placed within the tropici group but with a distinctive phylogenomic position and low average nucleotide identity (ANI). CCGE531 and CCGE532 had common phenotypic characteristics with tropici type B rhizobial symbionts. Genome synteny analysis and ANI showed that P. dumosus isolates had different chromids and our analysis suggests that chromids have independently evolved in different lineages of the Rhizobium genus. Finally, we considered that P. dumosus and Phaseolus vulgaris plants belong to the same cross-inoculation group since they have conserved symbiotic affinites for rhizobia.
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Affiliation(s)
| | | | | | - Ernesto Ormeño-Orrillo
- Laboratorio de Ecología Microbiana y Biotecnología, Departamento de Biología, Facultad de Ciencias, Universidad Nacional Agraria La Molina, Lima, Peru
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De Luca D, Cennamo P, Del Guacchio E, Di Novella R, Caputo P. Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity. Genetica 2017; 146:29-44. [PMID: 29030763 DOI: 10.1007/s10709-017-9994-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2017] [Accepted: 09/25/2017] [Indexed: 11/26/2022]
Abstract
Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.
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Affiliation(s)
- Daniele De Luca
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy.
| | - Paola Cennamo
- Facoltà di Lettere, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | - Emanuele Del Guacchio
- Facoltà di Scienze della Formazione, Università degli Studi Suor Orsola Benincasa di Napoli, Via Santa Caterina da Siena 37, 80135, Naples, Italy
| | | | - Paolo Caputo
- Dipartimento di Biologia, Università degli Studi di Napoli Federico II, via Foria 223, 80139, Naples, Italy
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Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A. Genomic history of the origin and domestication of common bean unveils its closest sister species. Genome Biol 2017; 18:60. [PMID: 28356141 PMCID: PMC5370463 DOI: 10.1186/s13059-017-1190-6] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 03/07/2017] [Indexed: 11/19/2022] Open
Abstract
Background Modern civilization depends on only a few plant species for its nourishment. These crops were derived via several thousands of years of human selection that transformed wild ancestors into high-yielding domesticated descendants. Among cultivated plants, common bean (Phaseolus vulgaris L.) is the most important grain legume. Yet, our understanding of the origins and concurrent shaping of the genome of this crop plant is limited. Results We sequenced the genomes of 29 accessions representing 12 Phaseolus species. Single nucleotide polymorphism-based phylogenomic analyses, using both the nuclear and chloroplast genomes, allowed us to detect a speciation event, a finding further supported by metabolite profiling. In addition, we identified ~1200 protein coding genes (PCGs) and ~100 long non-coding RNAs with domestication-associated haplotypes. Finally, we describe asymmetric introgression events occurring among common bean subpopulations in Mesoamerica and across hemispheres. Conclusions We uncover an unpredicted speciation event in the tropical Andes that gave rise to a sibling species, formerly considered the “wild ancestor” of P. vulgaris, which diverged before the split of the Mesoamerican and Andean P. vulgaris gene pools. Further, we identify haplotypes strongly associated with genes underlying the emergence of domestication traits. Our findings also reveal the capacity of a predominantly autogamous plant to outcross and fix loci from different populations, even from distant species, which led to the acquisition by domesticated beans of adaptive traits from wild relatives. The occurrence of such adaptive introgressions should be exploited to accelerate breeding programs in the near future. Electronic supplementary material The online version of this article (doi:10.1186/s13059-017-1190-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Martha Rendón-Anaya
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Josaphat M Montero-Vargas
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Soledad Saburido-Álvarez
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - Anna Vlasova
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Salvador Capella-Gutierrez
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - José Juan Ordaz-Ortiz
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico
| | - O Mario Aguilar
- Instituto de Biotecnología y Biología Molecular (IBBM), UNLP-CONICET, 1900, La Plata, Argentina
| | | | - Marta Santalla
- Mision Biológica de Galicia (MBG)-National Spanish Research Council (CSIC), 36080, Pontevedra, Spain
| | - Luis Delaye
- Departamento de Ingeniería Genética, Unidad Irapuato, Cinvestav, Irapuato, Guanajuato, Mexico
| | - Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, CA, 95616-8780, USA
| | - Robert Winkler
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, Cinvestav, 36821, Irapuato, Guanajuato, Mexico
| | - Roderic Guigó
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Dr. Aiguader 88, 08003, Barcelona, Spain
| | - Alfonso Delgado-Salinas
- Departamento de Botánica, Instituto de Biología, Universidad Nacional Autónoma de México, 04510, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados del IPN (Cinvestav), 36821, Irapuato, Guanajuato, Mexico.
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da Costa Neto VP, Mendes JBS, de Araújo ASF, de Alcântara Neto F, Bonifacio A, Rodrigues AC. Symbiotic performance, nitrogen flux and growth of lima bean (Phaseolus lunatus L.) varieties inoculated with different indigenous strains of rhizobia. Symbiosis 2017. [DOI: 10.1007/s13199-017-0475-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Complete Genome Sequence of Bradyrhizobium sp. Strain CCGE-LA001, Isolated from Field Nodules of the Enigmatic Wild Bean Phaseolus microcarpus. GENOME ANNOUNCEMENTS 2016; 4:4/2/e00126-16. [PMID: 26988045 PMCID: PMC4796124 DOI: 10.1128/genomea.00126-16] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the complete genome sequence of Bradyrhizobium sp. strain CCGE-LA001, a nitrogen-fixing bacterium isolated from nodules of Phaseolus microcarpus. Strain CCGE-LA001 represents the first sequenced bradyrhizobial strain obtained from a wild Phaseolus sp. Its genome revealed a large and novel symbiotic island.
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Parker MA, Jankowiak JG, Landrigan GK. Diversifying selection by Desmodiinae legume species onBradyrhizobiumsymbionts. FEMS Microbiol Ecol 2015; 91:fiv075. [DOI: 10.1093/femsec/fiv075] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2015] [Indexed: 11/14/2022] Open
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