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Genome Sequence of Bradyrhizobium japonicum E109, One of the Most Agronomically Used Nitrogen-Fixing Rhizobacteria in Argentina. GENOME ANNOUNCEMENTS 2015; 3:3/1/e01566-14. [PMID: 25700406 PMCID: PMC4335331 DOI: 10.1128/genomea.01566-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
We present here the complete genome sequence of Bradyrhizobium japonicum strain E109, one of the most used rhizobacteria for soybean inoculation in Argentina since the 1970s. The genome consists of a 9.22-Mbp single chromosome and contains several genes related to nitrogen fixation, phytohormone biosynthesis, and a rhizospheric lifestyle.
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Shiina Y, Itakura M, Choi H, Saeki Y, Hayatsu M, Minamisawa K. Relationship between soil type and N₂O reductase genotype (nosZ) of indigenous soybean bradyrhizobia: nosZ-minus populations are dominant in Andosols. Microbes Environ 2014; 29:420-6. [PMID: 25476067 PMCID: PMC4262367 DOI: 10.1264/jsme2.me14130] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2014] [Accepted: 10/14/2014] [Indexed: 11/29/2022] Open
Abstract
Bradyrhizobium japonicum strains that have the nosZ gene, which encodes N2O reductase, are able to mitigate N2O emissions from soils (15). To examine the distribution of nosZ genotypes among Japanese indigenous soybean bradyrhizobia, we isolated bradyrhizobia from the root nodules of soybean plants inoculated with 32 different soils and analyzed their nosZ and nodC genotypes. The 1556 resultant isolates were classified into the nosZ+/nodC+ genotype (855 isolates) and nosZ-/nodC+ genotype (701 isolates). The 11 soil samples in which nosZ- isolates significantly dominated (P < 0.05; the χ(2) test) were all Andosols (a volcanic ash soil prevalent in agricultural fields in Japan), whereas the 17 soil samples in which nosZ+ isolates significantly dominated were mainly alluvial soils (non-volcanic ash soils). This result was supported by a principal component analysis of environmental factors: the dominance of the nosZ- genotype was positively correlated with total N, total C, and the phosphate absorption coefficient in the soils, which are soil properties typical of Andosols. Internal transcribed spacer sequencing of representative isolates showed that the nosZ+ and nosZ- isolates of B. japonicum fell mainly into the USDA110 (BJ1) and USDA6 (BJ2) groups, respectively. These results demonstrated that the group lacking nosZ was dominant in Andosols, which can be a target soil type for an N2O mitigation strategy in soybean fields. We herein discussed how the nosZ genotypes of soybean bradyrhizobia depended on soil types in terms of N2O respiration selection and genomic determinants for soil adaptation.
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Affiliation(s)
- Yoko Shiina
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Hyunseok Choi
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
| | - Yuichi Saeki
- Department of Biochemistry and Applied Biosciences, Faculty of Agriculture, Miyazaki University, Miyazaki 889–2192,
Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3, Kannondai, Tsukuba, Ibaraki 305–8604,
Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai 980–8577,
Japan
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53
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Zuleta LFG, Cunha CDO, de Carvalho FM, Ciapina LP, Souza RC, Mercante FM, de Faria SM, Baldani JI, Straliotto R, Hungria M, de Vasconcelos ATR. The complete genome of Burkholderia phenoliruptrix strain BR3459a, a symbiont of Mimosa flocculosa: highlighting the coexistence of symbiotic and pathogenic genes. BMC Genomics 2014; 15:535. [PMID: 24972629 PMCID: PMC4101177 DOI: 10.1186/1471-2164-15-535] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 06/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Burkholderia species play an important ecological role related to xenobiosis, the promotion of plant growth, the biocontrol of agricultural diseases, and symbiotic and non-symbiotic biological nitrogen fixation. Here, we highlight our study as providing the first complete genome of a symbiotic strain of B. phenoliruptrix, BR3459a (=CLA1), which was originally isolated in Brazil from nodules of Mimosa flocculosa and is effective in fixing nitrogen in association with this leguminous species. RESULTS Genomic comparisons with other pathogenic and non-pathogenic Burkholderia strains grouped B. phenoliruptrix BR3459a with plant-associated beneficial and environmental species, although it shares a high percentage of its gene repertoire with species of the B. cepacia complex (Bcc) and "pseudomallei" group. The genomic analyses showed that the bce genes involved in exopolysaccharide production are clustered together in the same genomic region, constituting part of the Group III cluster of non-pathogenic bacteria. Regarding environmental stresses, we highlight genes that might be relevant in responses to osmotic, heat, cold and general stresses. Furthermore, a number of particularly interesting genes involved in the machinery of the T1SS, T2SS, T3SS, T4ASS and T6SS secretion systems were identified. The xenobiotic properties of strain BR3459a were also investigated, and some enzymes involved in the degradation of styrene, nitrotoluene, dioxin, chlorocyclohexane, chlorobenzene and caprolactam were identified. The genomic analyses also revealed a large number of antibiotic-related genes, the most important of which were correlated with streptomycin and novobiocin. The symbiotic plasmid showed high sequence identity with the symbiotic plasmid of B. phymatum. Additionally, comparative analysis of 545 housekeeping genes among pathogenic and non-pathogenic Burkholderia species strongly supports the definition of a new genus for the second branch, which would include BR3459a. CONCLUSIONS The analyses of B. phenoliruptrix BR3459a showed key property of fixing nitrogen that together with genes for high tolerance to environmental stresses might explain a successful strategy of symbiosis in the tropics. The strain also harbours interesting sets of genes with biotechnological potential. However, the resemblance of certain genes to those of pathogenic Burkholderia raise concerns about large-scale applications in agriculture or for bioremediation.
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Siqueira AF, Ormeño-Orrillo E, Souza RC, Rodrigues EP, Almeida LGP, Barcellos FG, Batista JSS, Nakatani AS, Martínez-Romero E, Vasconcelos ATR, Hungria M. Comparative genomics of Bradyrhizobium japonicum CPAC 15 and Bradyrhizobium diazoefficiens CPAC 7: elite model strains for understanding symbiotic performance with soybean. BMC Genomics 2014; 15:420. [PMID: 24888481 PMCID: PMC4070871 DOI: 10.1186/1471-2164-15-420] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2014] [Accepted: 05/20/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The soybean-Bradyrhizobium symbiosis can be highly efficient in fixing nitrogen, but few genomic sequences of elite inoculant strains are available. Here we contribute with information on the genomes of two commercial strains that are broadly applied to soybean crops in the tropics. B. japonicum CPAC 15 (=SEMIA 5079) is outstanding in its saprophytic capacity and competitiveness, whereas B. diazoefficiens CPAC 7 (=SEMIA 5080) is known for its high efficiency in fixing nitrogen. Both are well adapted to tropical soils. The genomes of CPAC 15 and CPAC 7 were compared to each other and also to those of B. japonicum USDA 6T and B. diazoefficiens USDA 110T. RESULTS Differences in genome size were found between species, with B. japonicum having larger genomes than B. diazoefficiens. Although most of the four genomes were syntenic, genome rearrangements within and between species were observed, including events in the symbiosis island. In addition to the symbiotic region, several genomic islands were identified. Altogether, these features must confer high genomic plasticity that might explain adaptation and differences in symbiotic performance. It was not possible to attribute known functions to half of the predicted genes. About 10% of the genomes was composed of exclusive genes of each strain, but up to 98% of them were of unknown function or coded for mobile genetic elements. In CPAC 15, more genes were associated with secondary metabolites, nutrient transport, iron-acquisition and IAA metabolism, potentially correlated with higher saprophytic capacity and competitiveness than seen with CPAC 7. In CPAC 7, more genes were related to the metabolism of amino acids and hydrogen uptake, potentially correlated with higher efficiency of nitrogen fixation than seen with CPAC 15. CONCLUSIONS Several differences and similarities detected between the two elite soybean-inoculant strains and between the two species of Bradyrhizobium provide new insights into adaptation to tropical soils, efficiency of N2 fixation, nodulation and competitiveness.
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Affiliation(s)
- Arthur Fernandes Siqueira
- />Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), C.P. 60001, Londrina, PR 86051-990 Brazil
- />Embrapa Soja, C.P. 231, Londrina, PR 86001-970 Brazil
| | - Ernesto Ormeño-Orrillo
- />Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos Mexico
| | - Rangel Celso Souza
- />Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Petrópolis, RJ 25651-071 Brazil
| | | | - Luiz Gonzaga Paula Almeida
- />Laboratório Nacional de Computação Científica, Rua Getúlio Vargas 333, Petrópolis, RJ 25651-071 Brazil
| | | | - Jesiane Stefânia Silva Batista
- />Department Structural, Molecular and Genetic Biology, Universidade Estadual de Ponta Grossa (UEPG), Av. General Carlos Cavalcanti 4748, Ponta Grossa, PR 84030-900 Brazil
| | | | | | | | - Mariangela Hungria
- />Department Biochemistry and Biotechnology, Universidade Estadual de Londrina (UEL), C.P. 60001, Londrina, PR 86051-990 Brazil
- />Embrapa Soja, C.P. 231, Londrina, PR 86001-970 Brazil
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Zhang XX, Guo HJ, Wang R, Sui XH, Zhang YM, Wang ET, Tian CF, Chen WX. Genetic divergence of bradyrhizobium strains nodulating soybeans as revealed by multilocus sequence analysis of genes inside and outside the symbiosis island. Appl Environ Microbiol 2014; 80:3181-90. [PMID: 24632260 PMCID: PMC4018923 DOI: 10.1128/aem.00044-14] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Accepted: 03/07/2014] [Indexed: 01/26/2023] Open
Abstract
The genus Bradyrhizobium has been considered to be a taxonomically difficult group. In this study, phylogenetics and evolutionary genetics analyses were used to investigate divergence levels among Bradyrhizobium strains nodulating soybeans in China. Eleven genospecies were identified by sequence analysis of three phylogenetic and taxonomic markers (SMc00019, thrA, and truA). This was also supported by analyses of eight genes outside the symbiosis island ("off-island" genes; SMc00019, thrA, truA, fabB, glyA, phyR, exoN, and hsfA). However, seven genes inside the symbiosis island ("island" genes; nifA, nifH, nodC, nodV, fixA, trpD, and rhcC2) showed contrasting lower levels of nucleotide diversity and recombination rates than did off-island genes. Island genes had significantly incongruent gene phylogenies compared to the species tree. Four phylogenetic clusters were observed in island genes, and the epidemic cluster IV (harbored by Bradyrhizobium japonicum, Bradyrhizobium diazoefficiens, Bradyrhizobium huanghuaihaiense, Bradyrhizobium liaoningense, Bradyrhizobium daqingense, Bradyrhizobium sp. I, Bradyrhizobium sp. III, and Bradyrhizobium sp. IV) was not found in Bradyrhizobium yuanmingense, Bradyrhizobium sp. II, or Bradyrhizobium elkanii. The gene flow level of island genes among genospecies is discussed in the context of the divergence level of off-island genes.
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Affiliation(s)
- Xing Xing Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Hui Juan Guo
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Rui Wang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Xin Hua Sui
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Yan Ming Zhang
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - En Tao Wang
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City, Mexico
| | - Chang Fu Tian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
| | - Wen Xin Chen
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
- Key Laboratory of Soil Microbiology, Ministry of Agriculture, China Agricultural University, Beijing, China
- Rhizobium Research Center, China Agricultural University, Beijing, China
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Geetha SJ, Joshi SJ. Engineering rhizobial bioinoculants: a strategy to improve iron nutrition. ScientificWorldJournal 2013; 2013:315890. [PMID: 24319357 PMCID: PMC3836376 DOI: 10.1155/2013/315890] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Accepted: 09/26/2013] [Indexed: 11/18/2022] Open
Abstract
Under field conditions, inoculated rhizobial strains are at a survival disadvantage as compared to indigenous strains. In order to out-compete native rhizobia it is not only important to develop strong nodulation efficiency but also increase their competence in the soil and rhizosphere. Competitive survival of the inoculated strain may be improved by employing strain selection and by genetic engineering of superior nitrogen fixing strains. Iron sufficiency is an important factor determining the survival and nodulation by rhizobia in soil. Siderophores, a class of ferric specific ligands that are involved in receptor specific iron transport into bacteria, constitute an important part of iron acquisition systems in rhizobia and have been shown to play a role in symbiosis as well as in saprophytic survival. Soils predominantly have iron bound to hydroxamate siderophores, a pool that is largely unavailable to catecholate-utilizing rhizobia. Outer membrane receptors for uptake of ferric hydroxamates include FhuA and FegA which are specific for ferrichrome siderophore. Increase in nodule occupancy and enhanced plant growth of the fegA and fhuA expressing engineered bioinoculants rhizobial strain have been reported. Engineering rhizobia for developing effective bioinoculants with improved ability to utilize heterologous siderophores could provide them with better iron acquisition ability and consequently, rhizospheric stability.
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Affiliation(s)
- S. J. Geetha
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
| | - Sanket J. Joshi
- Department of Biology, College of Science, Sultan Qaboos University, P.O. Box 36, Muscat 123, Oman
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Kumar D, Yadav AK, Kadimi PK, Nagaraj SH, Grimmond SM, Dash D. Proteogenomic analysis of Bradyrhizobium japonicum USDA110 using GenoSuite, an automated multi-algorithmic pipeline. Mol Cell Proteomics 2013; 12:3388-97. [PMID: 23882027 PMCID: PMC3820949 DOI: 10.1074/mcp.m112.027169] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 07/19/2013] [Indexed: 11/06/2022] Open
Abstract
We present GenoSuite, an integrated proteogenomic pipeline to validate, refine and discover protein coding genes using high-throughput mass spectrometry (MS) data from prokaryotes. To demonstrate the effectiveness of GenoSuite, we analyzed proteomics data of Bradyrhizobium japonicum (USDA110), a model organism to study agriculturally important rhizobium-legume symbiosis. Our analysis confirmed 31% of known genes, refined 49 gene models for their translation initiation site (TIS) and discovered 59 novel protein coding genes. Notably, a novel protein which redefined the boundary of a crucial cytochrome P450 system related operon was discovered, known to be highly expressed in the anaerobic symbiotic bacteroids. A focused analysis on N-terminally acetylated peptides indicated downstream TIS for gene blr0594. Finally, ortho-proteogenomic analysis revealed three novel genes in recently sequenced B. japonicum USDA6(T) genome. The discovery of large number of missing genes and correction of gene models have expanded the proteomic landscape of B. japonicum and presents an unparalleled utility of proteogenomic analyses and versatility of GenoSuite for annotating prokaryotic genomes including pathogens.
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Affiliation(s)
- Dhirendra Kumar
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Amit Kumar Yadav
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Puneet Kumar Kadimi
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
| | - Shivashankar H. Nagaraj
- §Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Sean M. Grimmond
- §Queensland Centre for Medical Genomics, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, 4072, Australia
| | - Debasis Dash
- From the ‡G.N. Ramachandran Knowledge Center for Genome Informatics, CSIR-Institute of Genomics and Integrative Biology, South Campus, Sukhdev Vihar, Mathura Road, Delhi 110025, India
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58
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Delamuta JRM, Ribeiro RA, Ormeño-Orrillo E, Melo IS, Martínez-Romero E, Hungria M. Polyphasic evidence supporting the reclassification of
Bradyrhizobium japonicum
group Ia strains as
Bradyrhizobium
diazoefficiens sp. nov. Int J Syst Evol Microbiol 2013; 63:3342-3351. [DOI: 10.1099/ijs.0.049130-0] [Citation(s) in RCA: 202] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bradyrhizobium japonicum
was described from soybean root-nodule bacterial isolates. Since its description, several studies have revealed heterogeneities among rhizobia assigned to this species. Strains assigned to
B. japonicum
group Ia have been isolated in several countries, and many of them are outstanding soybean symbionts used in inoculants worldwide, but they have also been isolated from other legume hosts. Here, we summarize published studies that indicate that group Ia strains are different from the
B. japonicum
type strain USDA 6T and closely related strains, and present new morphophysiological, genotypic and genomic evidence to support their reclassification into a novel species, for which the name
Bradyrhizobium
diazoefficiens sp. nov. is proposed. The type strain of the novel species is the well-studied strain USDA 110T ( = IAM 13628T = CCRC 13528T = NRRL B-4361T = NRRL B-4450T = TAL 102T = BCRC 13528T = JCM 10833T = TISTR 339T = SEMIA 5032T = 3I1B110T = ACCC 15034T = CCT 4249T = NBRC 14792T = R-12974T = CNPSo 46T).
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Affiliation(s)
- Jakeline Renata Marçon Delamuta
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Renan Augusto Ribeiro
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
| | - Ernesto Ormeño-Orrillo
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | | | | | - Mariangela Hungria
- Universidade Estadual de Londrina, Dept of Microbiology, C.P. 60001, 86051-990 Londrina, Paraná, Brazil
- Embrapa Soja, C.P. 231, 86001-970 Londrina, Paraná, Brazil
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Kasai-Maita H, Hirakawa H, Nakamura Y, Kaneko T, Miki K, Maruya J, Okazaki S, Tabata S, Saeki K, Sato S. Commonalities and differences among symbiosis islands of three Mesorhizobium loti strains. Microbes Environ 2013; 28:275-8. [PMID: 23666538 PMCID: PMC4070662 DOI: 10.1264/jsme2.me12201] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To shed light on the breadth of the host range of Mesorhizobium loti strain NZP2037, we determined the sequence of the NZP2037 symbiosis island and compared it with those of strain MAFF303099 and R7A islands. The determined 533 kb sequence of NZP2037 symbiosis island, on which 504 genes were predicted, implied its integration into a phenylalanine-tRNA gene and subsequent genome rearrangement. Comparative analysis revealed that the core regions of the three symbiosis islands consisted of 165 genes. We also identified several NZP2037-specific genes with putative functions in nodulation-related events, suggesting that these genes contribute to broaden the host range of NZP2037.
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Affiliation(s)
- Hiroko Kasai-Maita
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2–6–7 Kazusa-kamatari Kisarazu, Chiba 292–0818, Japan
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60
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Kimbrel JA, Thomas WJ, Jiang Y, Creason AL, Thireault CA, Sachs JL, Chang JH. Mutualistic co-evolution of type III effector genes in Sinorhizobium fredii and Bradyrhizobium japonicum. PLoS Pathog 2013; 9:e1003204. [PMID: 23468637 PMCID: PMC3585131 DOI: 10.1371/journal.ppat.1003204] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 01/08/2013] [Indexed: 12/16/2022] Open
Abstract
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing model, conflicts between mutualist and host are largely resolved and the interaction is characterized by evolutionary stasis. We tested these opposing frameworks in two lineages of mutualistic rhizobia, Sinorhizobium fredii and Bradyrhizobium japonicum. To examine genes demonstrably important for host-interactions we coupled the mining of genome sequences to a comprehensive functional screen for type III effector genes, which are necessary for many Gram-negative pathogens to infect their hosts. We demonstrate that the rhizobial type III effector genes exhibit a surprisingly high degree of conservation in content and sequence that is in contrast to those of a well characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the context of the relatively high genome-wide diversity of rhizobia. The evolution of rhizobial type III effectors is inconsistent with the molecular arms race paradigm. Instead, our results reveal that these loci are relatively static in rhizobial lineages and suggest that fitness conflicts between rhizobia mutualists and their host plants have been largely resolved.
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Affiliation(s)
- Jeffrey A. Kimbrel
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - William J. Thomas
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Yuan Jiang
- Department of Statistics, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
| | - Allison L. Creason
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
| | - Caitlin A. Thireault
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
| | - Joel L. Sachs
- Department of Biology, University of California-Riverside, Riverside, California, United States of America
| | - Jeff H. Chang
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon, United States of America
- Molecular and Cellular Biology Program, Oregon State University, Corvallis, Oregon, United States of America
- Center for Genome Research and Biocomputing, Oregon State University, Corvallis, Oregon, United States of America
- * E-mail:
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61
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Genome analysis suggests that the soil oligotrophic bacterium Agromonas oligotrophica (Bradyrhizobium oligotrophicum) is a nitrogen-fixing symbiont of Aeschynomene indica. Appl Environ Microbiol 2013; 79:2542-51. [PMID: 23396330 DOI: 10.1128/aem.00009-13] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Agromonas oligotrophica (Bradyrhizobium oligotrophicum) S58(T) is a nitrogen-fixing oligotrophic bacterium isolated from paddy field soil that is able to grow in extra-low-nutrient environments. Here, the complete genome sequence of S58 was determined. The S58 genome was found to comprise a circular chromosome of 8,264,165 bp with an average GC content of 65.1% lacking nodABC genes and the typical symbiosis island. The genome showed a high level of similarity to the genomes of Bradyrhizobium sp. ORS278 and Bradyrhizobium sp. BTAi1, including nitrogen fixation and photosynthesis gene clusters, which nodulate an aquatic legume plant, Aeschynomene indica, in a Nod factor-independent manner. Although nonsymbiotic (brady)rhizobia are significant components of rhizobial populations in soil, we found that most genes important for nodule development (ndv) and symbiotic nitrogen fixation (nif and fix) with A. indica were well conserved between the ORS278 and S58 genomes. Therefore, we performed inoculation experiments with five A. oligotrophica strains (S58, S42, S55, S72, and S80). Surprisingly, all five strains of A. oligotrophica formed effective nitrogen-fixing nodules on the roots and/or stems of A. indica, with differentiated bacteroids. Nonsymbiotic (brady)rhizobia are known to be significant components of rhizobial populations without a symbiosis island or symbiotic plasmids in soil, but the present results indicate that soil-dwelling A. oligotrophica generally possesses the ability to establish symbiosis with A. indica. Phylogenetic analyses suggest that Nod factor-independent symbiosis with A. indica is a common trait of nodABC- and symbiosis island-lacking strains within the members of the photosynthetic Bradyrhizobium clade, including A. oligotrophica.
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Tang J, Bromfield ESP, Rodrigue N, Cloutier S, Tambong JT. Microevolution of symbiotic Bradyrhizobium populations associated with soybeans in east North America. Ecol Evol 2012; 2:2943-61. [PMID: 23301163 PMCID: PMC3538991 DOI: 10.1002/ece3.404] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2012] [Accepted: 09/17/2012] [Indexed: 11/22/2022] Open
Abstract
Microevolution and origins of Bradyrhizobium populations associated with soybeans at two field sites (A and B, 280 km apart in Canada) with contrasting histories of inoculation was investigated using probabilistic analyses of six core (housekeeping) gene sequences. These analyses supported division of 220 isolates in five lineages corresponding either to B. japonicum groups 1 and 1a or to one of three novel lineages within the genus Bradyrhizobium. None of the isolates from site A and about 20% from site B (the only site with a recent inoculation history) were attributed to inoculation sources. The data suggest that most isolates were of indigenous origin based on sequence analysis of 148 isolates of soybean-nodulating bacteria from native legumes (Amphicarpaea bracteata and Desmodium canadense). Isolates from D. canadense clustered with B. japonicum group 1, whereas those from A. bracteata were placed in two novel lineages encountered at soybean field sites. One of these novel lineages predominated at soybean sites and exhibited a significant clonal expansion likely reflecting selection by the plant host. Homologous recombination events detected in the 35 sequence types from soybean sites had an effect on genetic diversification that was approximately equal to mutation. Interlineage transfer of core genes was infrequent and mostly attributable to gyrB that had a history of frequent recombination. Symbiotic gene sequences (nodC and nifH) of isolates from soybean sites and native legumes clustered in two lineages corresponding to B. japonicum and B. elkani with the inheritance of these genes appearing predominantly by vertical transmission. The data suggest that soybean-nodulating bacteria associated with native legumes represent a novel source of ecologically adapted bacteria for soybean inoculation.
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Affiliation(s)
- Jie Tang
- Agriculture and Agri-Food Canada 960 Carling Ave, Ottawa, Ontario, Canada, K1A 0C6
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Aserse AA, Räsänen LA, Aseffa F, Hailemariam A, Lindström K. Phylogenetically diverse groups of Bradyrhizobium isolated from nodules of Crotalaria spp., Indigofera spp., Erythrina brucei and Glycine max growing in Ethiopia. Mol Phylogenet Evol 2012; 65:595-609. [PMID: 22842091 DOI: 10.1016/j.ympev.2012.07.008] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/09/2012] [Accepted: 07/14/2012] [Indexed: 12/16/2022]
Abstract
Ethiopian Bradyrhizobium strains isolated from root nodules of Crotalaria spp., Indigofera spp., Erythina brucei and soybean (Glycine max) represented genetically diverse phylogenetic groups of the genus Bradyrhizobium. Strains were characterized using the amplified fragment length polymorphism fingerprinting technique (AFLP) and multilocus sequence analysis (MLSA) of core and symbiotic genes. Based on phylogenetic analyses of concatenated recA-glnII-rpoB-16S rRNA genes sequences, Bradyrhizobium strains were distributed into fifteen phylogenetic groups under B. japonicum and B. elkanii super clades. Some of the isolates belonged to the species B. yuanmingense, B. elkanii and B. japonicum type I. However, the majority of the isolates represented unnamed Bradyrhizobium genospecies and of these, two unique lineages that most likely represent novel Bradyrhizobium species were identified among Ethiopian strains. The nodulation nodA gene sequence analysis revealed that all Ethiopian Bradyrhizobium isolates belonged to nodA sub-clade III.3. Strains were further classified into 14 groups together with strains from Africa, as well as some originating from the other tropical and subtropics regions. Strains were also clustered into 14 groups in nodY/K phylogeny similarly to the nodA tree. The nifH phylogenies of the Ethiopian Bradyrhizobium were generally also congruent with the nodA gene phylogeny, supporting the monophyletic origin of the symbiotic genes in Bradyrhizobium. The phylogenies of nodA and nifH genes were also partially congruent with that inferred from the concatenated core genes sequences, reflecting that the strains obtained their symbiotic genes vertically from their ancestor as well as horizontally from more distantly related Bradyrhizobium species.
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Affiliation(s)
- Aregu Amsalu Aserse
- University of Helsinki, Department of Food and Environmental Sciences, POB 56, FIN-00014 Helsinki, Finland.
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Okubo T, Tsukui T, Maita H, Okamoto S, Oshima K, Fujisawa T, Saito A, Futamata H, Hattori R, Shimomura Y, Haruta S, Morimoto S, Wang Y, Sakai Y, Hattori M, Aizawa SI, Nagashima KVP, Masuda S, Hattori T, Yamashita A, Bao Z, Hayatsu M, Kajiya-Kanegae H, Yoshinaga I, Sakamoto K, Toyota K, Nakao M, Kohara M, Anda M, Niwa R, Jung-Hwan P, Sameshima-Saito R, Tokuda SI, Yamamoto S, Yamamoto S, Yokoyama T, Akutsu T, Nakamura Y, Nakahira-Yanaka Y, Hoshino YT, Hirakawa H, Mitsui H, Terasawa K, Itakura M, Sato S, Ikeda-Ohtsubo W, Sakakura N, Kaminuma E, Minamisawa K. Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs. Microbes Environ 2012; 27:306-15. [PMID: 22452844 PMCID: PMC4036050 DOI: 10.1264/jsme2.me11321] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2011] [Accepted: 02/28/2012] [Indexed: 11/12/2022] Open
Abstract
Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.
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Affiliation(s)
- Takashi Okubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Takahiro Tsukui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Hiroko Maita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Shinobu Okamoto
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Kenshiro Oshima
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Takatomo Fujisawa
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Akihiro Saito
- Department of Material and Life Science, Faculty of Science and Technology, Shizuoka Institute of Science and Technology 2200–2 Toyosawa, Fukuroi, Shizuoka 437–8555, Japan
| | - Hiroyuki Futamata
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Reiko Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Yumi Shimomura
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Shin Haruta
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sho Morimoto
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yong Wang
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Yoriko Sakai
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Masahira Hattori
- Graduate School of Frontier Sciences, University of Tokyo, 5–1–5, Kashiwa-no-ha, Kashiwa, Chiba 277–8561, Japan
| | - Shin-ichi Aizawa
- Department of Life Sciences, Prefectural University of Hiroshima, 562 Nanatsuka, Shobara, Hiroshima 727–0023, Japan
| | - Kenji V. P. Nagashima
- Graduate School of Science and Engineering, Tokyo Metropolitan University, 1–1 Minami-Osawa, Hachioji-shi, Tokyo 192–0397, Japan
| | - Sachiko Masuda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Tsutomu Hattori
- Attic Lab, 1–6–2–401 Komegafukuro, Aobaku, Sendai, Miyagi 980–0813, Japan
| | - Akifumi Yamashita
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Zhihua Bao
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Masahito Hayatsu
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hiromi Kajiya-Kanegae
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Ikuo Yoshinaga
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Kazunori Sakamoto
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba 271–8510, Japan
| | - Koki Toyota
- Tokyo University of Agriculture and Technology, 2–24–16, Naka, Koganei, Tokyo 184–8588, Japan
| | - Mitsuteru Nakao
- Database Center for Life Science (DBCLS), Research Organization of Information and Systems (ROIS), 2–11–16 Yayoi, Bunkyo-ku, Tokyo 113–0032, Japan
| | - Mitsuyo Kohara
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Mizue Anda
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Rieko Niwa
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Park Jung-Hwan
- Graduate School of Agriculture, Kyoto University, Oiwake-cho, Kitashirakawa, Sakyo-ku, Kyoto 606–8502, Japan
| | - Reiko Sameshima-Saito
- Faculty of Agriculture, Shizuoka University, 836 Ohya, Suruga-ku, Shizuoka 422–8529, Japan
| | - Shin-ichi Tokuda
- National Institute of Vegetable and Tea Sciences, National Agriculture and Food Research Organization, 3–1–1 Kannondai, Tsukuba, Ibaraki 305–8666, Japan
| | - Sumiko Yamamoto
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Syuji Yamamoto
- Department of Material Science and Chemical Engineering, Shizuoka University, 3–5–1 Jyohoku, Naka-ku, Hamamatsu, Shizuoka, 432–8561, Japan
| | - Tadashi Yokoyama
- Institute of Agriculture, Tokyo university of Agriculture and Technology, 3–5–8 Saiwaicho, Fuchu, Tokyo 183–8509, Japan
| | - Tomoko Akutsu
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Yasukazu Nakamura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Yuka Nakahira-Yanaka
- Graduate School of Life and Environment Sciences, University of Tsukuba, 1–1–1 Ten-noudai, Tsukuba, Ibaraki 305–8572, Japan
| | - Yuko Takada Hoshino
- National Institute for Agro-Environmental Sciences, 3–1–3 Kannondai, Tsukuba, Ibaraki 305–8604, Japan
| | - Hideki Hirakawa
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Hisayuki Mitsui
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Kimihiro Terasawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Manabu Itakura
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Shusei Sato
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
- Laboratory for Plant Genome Informatics, Kazusa DNA Research Institute, 2–6–7 Kazusakamatari, Kisarazu, Chiba 292–0818, Japan
| | - Wakako Ikeda-Ohtsubo
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
| | - Natsuko Sakakura
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Eli Kaminuma
- Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization for Information and Systems, Yata, Mishima, Shizuoka 411–85, Japan
| | - Kiwamu Minamisawa
- Graduate School of Life Sciences, Tohoku University, 2–1–1 Katahira, Aoba-ku, Sendai, Miyagi 980–8577, Japan
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