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- A Genome-Wide Identification of Genes Potentially Associated with Host Specificity of Brucella Species
- Kyung Mo Kim , Kyu-Won Kim , Samsun Sung , Heebal Kim
- J. Microbiol. 2011;49(5):768-775. Published online November 9, 2011
- DOI: https://doi.org/10.1007/s12275-011-1084-3
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Abstract
- Brucella species are facultative intracellular pathogenic α-Proteobacteria that can cause brucellosis in humans and domestic animals. The clinical and veterinary importance of the bacteria has led to well established studies on the molecular mechanisms of Brucella infection of host organisms. However, to date, no genome-wide study has scanned for genes related to the host specificity of Brucella spp. The majority of bacterial genes related to specific environmental adaptations such as host specificity are well-known to have evolved under positive selection pressure. We thus detected signals of positive selection for individual orthologous genes among Brucella genomes and identified genes related to host specificity. We first determined orthologous sets from seven completely sequenced Brucella genomes using the Reciprocal Best Hits (RBH). A maximum likelihood analysis based on the branch-site test was accomplished to examine the presence of positive selection signals, which was subsequently confirmed by phylogenetic analysis. Consequently, 12 out of 2,033 orthologous genes were positively selected by specific Brucella lineages, each of which belongs to a particular animal host. Extensive literature reviews revealed that half of these computationally identified genes are indeed involved in Brucella host specificity. We expect that this genome-wide approach based on positive selection may be reliably used to screen for genes related to environmental adaptation of a particular species and that it will provide a set of appropriate candidate genes.
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Citations
Citations to this article as recorded by
- Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae)
Abigail R. Mazie, David A. Baum
Molecular Phylogenetics and Evolution.2016; 100: 31. CrossRef - Identification of Recombination and Positively Selected Genes in Brucella
Udayakumar S. Vishnu, Jagadesan Sankarasubramanian, Jayavel Sridhar, Paramasamy Gunasekaran, Jeyaprakash Rajendhran
Indian Journal of Microbiology.2015; 55(4): 384. CrossRef - Comparison of Brucella canis genomes isolated from different countries shows multiple variable regions
Miryan Margot Sánchez-Jiménez, Juan Pablo Isaza, Juan F. Alzate, Martha Olivera-Angel
Genomics.2015; 106(1): 43. CrossRef - Complete Genome Sequence of Brucella canis Strain 118, a Strain Isolated from Canine
Guangjun Gao, Jing Li, Tiefeng Li, Zhengfang Zhang, Liping Wang, Xitong Yuan, Yufei Wang, Jie Xu, Yuehua Ke, Liuyu Huang, Dali Wang, Zeliang Chen, Xingran Xu
Journal of Bacteriology.2012; 194(23): 6680. CrossRef - Complete Genome Sequence of Brucella canis BCB018, a Strain Isolated from a Human Patient
Yufei Wang, Yuehua Ke, Qing Zhen, Xitong Yuan, Jie Xu, Yefeng Qiu, Zhoujia Wang, Tiefeng Li, Dali Wang, Liuyu Huang, Zeliang Chen
Journal of Bacteriology.2012; 194(23): 6697. CrossRef
- Clade-specific positive selection on a developmental gene: BRANCHLESS TRICHOME and the evolution of stellate trichomes in Physaria (Brassicaceae)
- Distinctive Endophytic Fungal Assemblage in Stems of Wild Rice (Oryza granulata) in China with Special Reference to Two Species of Muscodor (Xylariaceae)
- Zhi-lin Yuan , Zhen-zhu Su , Li-juan Mao , Yang-qing Peng , Guan-mei Yang , Fu-cheng Lin , Chu-long Zhang
- J. Microbiol. 2011;49(1):15-23. Published online March 3, 2011
- DOI: https://doi.org/10.1007/s12275-011-0213-3
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- 25 Crossref
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Abstract
- Ecological niches in the rhizosphere and phyllosphere of grasses capable of sustaining endophytes have been extensively studied. In contrast, little information regarding the identity and functions of endophytic fungi in stems is available. In this study, we investigated the taxonomic affinities, diversity, and host specificities of culturable endophytes in stems of wild rice (Oryza granulata) in China. Seventy-four isolates were recovered. Low recovery rate (11.7%) indicated that there were relatively few sites for fungal infection. Identification using morphology, morphospecies sorting, and molecular techniques resulted in classification into 50 taxa, 36 of which were recovered only once. Nucleotide sequence similarity analysis indicated that 30% of the total taxa recovered were highly divergent from known species and thus may represent lineages new to science. Most of the taxa were classified as members of the classes Sordariomycetes or Dothideomycetes (mainly in Pleosporales). The presence of Arthrinium and Magnaporthaceae species, most often associated with poaceous plants, suggested a degree of host specificity. A polyphasic approach was employed to identify two Muscodor taxa based on (i) ITS and RPB2 phylogenies, (ii) volatile compounds produced, and (iii) an in vitro bioassay of antifungal activity. This to our knowledge is only the second report regarding the isolation of Muscodor spp. in China. Therefore, we hypothesize that wild plants represent a huge reservoir of unknown fungi. The prevalence, novelty, and species-specificity of unique isolates necessitate a reevaluation of their contribution to ecosystem function and fungal biodiversity.
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Citations
Citations to this article as recorded by- Prospects of fungal endophytes for stress mitigation in rice (Oryza sativa L.)
Boby Vattekkattu Unnikrishnan, Mahesh Mohan
Oryza-An International Journal on Rice.2022; 59(3): 309. CrossRef - Pest categorisation of Colletotrichum aenigma, C. alienum, C. perseae, C. siamense and C. theobromicola
Claude Bragard, Paula Baptista, Elisavet Chatzivassiliou, Francesco Di Serio, Paolo Gonthier, Josep Anton Jaques Miret, Annemarie Fejer Justesen, Alan MacLeod, Christer Sven Magnusson, Panagiotis Milonas, Juan A Navas‐Cortes, Stephen Parnell, Roel Potting
EFSA Journal.2022;[Epub] CrossRef - Phytotoxic compounds from endophytic fungi
Martha Lydia Macías-Rubalcava, Monserrat Yesenia Garrido-Santos
Applied Microbiology and Biotechnology.2022; 106(3): 931. CrossRef - Cross-pathogenicity of Colletotrichum isolates on tropical fruit species in Brazil
André Freire Cruz, Geleta Dugassa Barka, Luiz Eduardo Bassay Blum
Archives of Phytopathology and Plant Protection.2021; 54(5-6): 295. CrossRef - Endophytic microbes from Nigerian ethnomedicinal plants: a potential source for bioactive secondary metabolites—a review
Chijioke E. Ezeobiora, Nwamaka H. Igbokwe, Dina H. Amin, Udoma E. Mendie
Bulletin of the National Research Centre.2021;[Epub] CrossRef - Life on the Rocks: First Insights Into the Microbiota of the Threatened Aquatic Rheophyte Hanseniella heterophylla
Witoon Purahong, Shakhawat Hossen, Ali Nawaz, Dolaya Sadubsarn, Benjawan Tanunchai, Sven Dommert, Matthias Noll, La-aw Ampornpan, Petcharat Werukamkul, Tesfaye Wubet
Frontiers in Plant Science.2021;[Epub] CrossRef - Elucidation of the life cycle of the endophytic genus Muscodor and its transfer to Induratia in Induratiaceae fam. nov., based on a polyphasic taxonomic approach
Milan C. Samarakoon, Benjarong Thongbai, Kevin D. Hyde, Mark Brönstrup, Ulrike Beutling, Christopher Lambert, Andrew N. Miller, Jian-Kui (Jack) Liu, Itthayakorn Promputtha, Marc Stadler
Fungal Diversity.2020; 101(1): 177. CrossRef - Responses of the species complex Fallopia × bohemica to single-metal contaminations to Cd, Cr or Zn: growth traits, metal accumulation and secondary metabolism
Louise Barberis, Wilfried Chevalier, Marie-Laure Toussaint, Philippe Binet, Florence Piola, Serge Michalet
Environmental Monitoring and Assessment.2020;[Epub] CrossRef - Plant host and drought shape the root associated fungal microbiota in rice
Beatriz Andreo-Jimenez, Philippe Vandenkoornhuyse, Amandine Lê Van, Arvid Heutinck, Marie Duhamel, Niteen Kadam, Krishna Jagadish, Carolien Ruyter-Spira, Harro Bouwmeester
PeerJ.2019; 7: e7463. CrossRef - Plant-mycorrhizal fungi interaction and response to inoculation with different growth-promoting fungi
Carlos Vergara, Karla Emanuelle Campos Araujo, Sônia Regina de Souza, Nivaldo Schultz, Orivaldo José Saggin Júnior, Marcus Vinícius Loss Sperandio, Jerri Édson Zilli
Pesquisa Agropecuária Brasileira.2019;[Epub] CrossRef - Identification and characterization of new Muscodor endophytes from gramineous plants in Xishuangbanna, China
Li‐Juan Mao, Jia‐Jie Chen, Chen‐Yang Xia, Xiao‐Xiao Feng, De‐Dong Kong, Zhen‐Yu Qi, Feng Liu, Dian Chen, Fu‐Cheng Lin, Chu‐Long Zhang
MicrobiologyOpen.2019;[Epub] CrossRef - Brief Review on Fungal Endophytes
Rohit Shankar Mane, Padmaa Milaap Paarakh, Ankala Basappa Vedamurthy
International Journal of Secondary Metabolite.2018; 5(4): 288. CrossRef - Contribution of dark septate fungi to the nutrient uptake and growth of rice plants
Carlos Vergara, Karla Emanuelle Campos Araujo, Luiziene Soares Alves, Sônia Regina de Souza, Leandro Azevedo Santos, Claudete Santa-Catarina, Krisle da Silva, Gilmara Maria Duarte Pereira, Gustavo Ribeiro Xavier, Jerri Édson Zilli
Brazilian Journal of Microbiology.2018; 49(1): 67. CrossRef - Endophytic fungal community of Dysphania ambrosioides from two heavy metal‐contaminated sites: evaluated by culture‐dependent and culture‐independent approaches
Shobhika Parmar, Qiaohong Li, Ying Wu, Xinya Li, Jinping Yan, Vijay K. Sharma, Yunlin Wei, Haiyan Li
Microbial Biotechnology.2018; 11(6): 1170. CrossRef - Secondary structure prediction of ITS rRNA region and molecular phylogeny: an integrated approach for the precise speciation of Muscodor species
Neha Kapoor, Lokesh Gambhir, Sanjai Saxena
Annals of Microbiology.2018; 68(11): 763. CrossRef - Endophytic fungi harbored in the root of Sophora tonkinensis Gapnep: Diversity and biocontrol potential against phytopathogens
Yu Qun Yao, Fang Lan, Yun Ming Qiao, Ji Guang Wei, Rong Shao Huang, Liang Bo Li
MicrobiologyOpen.2017;[Epub] CrossRef - Dark Septate Endophytic Fungi Help Tomato to Acquire Nutrients from Ground Plant Material
Carlos Vergara, Karla E. C. Araujo, Segundo Urquiaga, Nivaldo Schultz, Fabiano de Carvalho Balieiro, Peter S. Medeiros, Leandro A. Santos, Gustavo R. Xavier, Jerri E. Zilli
Frontiers in Microbiology.2017;[Epub] CrossRef - Antifungal, anti-oomycete and phytotoxic effects of volatile organic compounds from the endophytic fungusXylariasp. strain PB3f3 isolated fromHaematoxylon brasiletto
B.L. Sánchez-Ortiz, R.E. Sánchez-Fernández, G. Duarte, P. Lappe-Oliveras, M.L. Macías-Rubalcava
Journal of Applied Microbiology.2016; 120(5): 1313. CrossRef - Phylogenetic diversity of culturable endophytic fungi in Dongxiang wild rice (Oryza rufipogon Griff), detection of polyketide synthase gene and their antagonistic activity analysis
Ya Wang, Bo Liang Gao, Xi Xi Li, Zhi Bin Zhang, Ri Ming Yan, Hui Lin Yang, Du Zhu
Fungal Biology.2015; 119(11): 1032. CrossRef - Identification of Acremonium isolates from grapevines and evaluation of their antagonism towards Plasmopara viticola
Sandra Lo Piccolo, Antonio Alfonzo, Selene Giambra, Gaetano Conigliaro, Luis V. Lopez-Llorca, Santella Burruano
Annals of Microbiology.2015; 65(4): 2393. CrossRef - Plant Bioactive Metabolites and Drugs Produced by Endophytic Fungi of Spermatophyta
Rosario Nicoletti, Antonio Fiorentino
Agriculture.2015; 5(4): 918. CrossRef - Endophytic Diaporthe from Southeast China are genetically diverse based on multi-locus phylogeny analyses
Jiaying Wang, Xihui Xu, Lijuan Mao, Jiaping Lao, Fucheng Lin, Zhilin Yuan, Chulong Zhang
World Journal of Microbiology and Biotechnology.2014; 30(1): 237. CrossRef - The Colletotrichum boninense species complex
U. Damm, P.F. Cannon, J.H.C. Woudenberg, P.R. Johnston, B.S. Weir, Y.P. Tan, R.G. Shivas, P.W. Crous
Studies in Mycology.2012; 73: 1. CrossRef - Current perspectives on the volatile-producing fungal endophytes
Yuan Zhi-Lin, Chen Yi-Cun, Xu Bai-Ge, Zhang Chu-Long
Critical Reviews in Biotechnology.2012; 32(4): 363. CrossRef - Colletotrichum – current status and future directions
P.F. Cannon, U. Damm, P.R. Johnston, B.S. Weir
Studies in Mycology.2012; 73: 181. CrossRef
- Prospects of fungal endophytes for stress mitigation in rice (Oryza sativa L.)
- Propagation of Bombyx mori Nucleopolyhedrovirus in Nonpermissive Insect Cell Lines
- Soo-Dong Woo , Jong Yul Roh , Jae Young Choi , Byung Rae Jin
- J. Microbiol. 2007;45(2):133-138.
- DOI: https://doi.org/2522 [pii]
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Abstract
- This study addresses the susceptibility of Spodoptera frugiperda (Sf9 and Sf21), Trichoplusia ni (Hi5), and S. exigua (Se301) cells to the Bombyx mori nucleopolyhedrovirus (BmNPV). Although these cells have classically been considered nonpermissive to BmNPV, the cytopathic effect, an increase in viral yield, and viral DNA synthesis by BmNPV were observed in Sf9, Sf21, and Hi5 cells, but not in Se301 cells. Very late gene expression by BmNPV in these cell lines was also detected via β-galactosidase expression under the control of the polyhedrin promoter. Sf9 cells were most susceptible to BmNPV in all respects, followed by Sf21 and Hi5 cells in decreasing order, while the Se301 cells evidenced no distinct viral replication. This particular difference in viral susceptibility in each of the cell lines can be utilized for our understanding of the mechanisms underlying the host specificity of NPVs.
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