The structure and function of the global citrus rhizosphere microbiome

[1]  Falk Hildebrand,et al.  Structure and function of the global topsoil microbiome , 2018, Nature.

[2]  Matthias Erb,et al.  Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota , 2018, Nature Communications.

[3]  A. Mchardy,et al.  Modular Traits of the Rhizobiales Root Microbiota and Their Evolutionary Relationship with Symbiotic Rhizobia , 2018, Cell host & microbe.

[4]  William A. Walters,et al.  Large-scale replicated field study of maize rhizosphere identifies heritable microbes , 2018, Proceedings of the National Academy of Sciences.

[5]  Y. Onoda,et al.  Core microbiomes for sustainable agroecosystems , 2018, Nature Plants.

[6]  S. Hacquard,et al.  Microbial interactions within the plant holobiont , 2018, Microbiome.

[7]  J. Dopazo,et al.  Genomics of the origin and evolution of Citrus , 2018, Nature.

[8]  N. Fierer,et al.  A global atlas of the dominant bacteria found in soil , 2018, Science.

[9]  D. Daffonchio,et al.  Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality , 2018, Microbiome.

[10]  F. Botha,et al.  Field study reveals core plant microbiota and relative importance of their drivers , 2018, Environmental microbiology.

[11]  Yunzeng Zhang,et al.  Characterization of Antimicrobial-Producing Beneficial Bacteria Isolated from Huanglongbing Escape Citrus Trees , 2017, Front. Microbiol..

[12]  Derek S. Lundberg,et al.  Genomic features of bacterial adaptation to plants , 2017, Nature Genetics.

[13]  Suisha Liang,et al.  Taxonomic structure and functional association of foxtail millet root microbiome , 2017, GigaScience.

[14]  Nian Wang,et al.  Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome , 2017, Microbiome.

[15]  M. Ragan,et al.  Evolutionary conservation of a core root microbiome across plant phyla along a tropical soil chronosequence , 2017, Nature Communications.

[16]  J. Setubal,et al.  The Candidatus Liberibacter-Host Interface: Insights into Pathogenesis Mechanisms and Disease Control. , 2017, Annual review of phytopathology.

[17]  Omri M. Finkel,et al.  Understanding and exploiting plant beneficial microbes. , 2017, Current opinion in plant biology.

[18]  P. Lemanceau,et al.  Let the Core Microbiota Be Functional. , 2017, Trends in plant science.

[19]  M. Bosse,et al.  Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits , 2017, The ISME Journal.

[20]  J. Leach,et al.  Communication in the Phytobiome , 2017, Cell.

[21]  Y. Ruan,et al.  Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction , 2017, Nature Genetics.

[22]  Jesse R. Zaneveld,et al.  Normalization and microbial differential abundance strategies depend upon data characteristics , 2017, Microbiome.

[23]  J. Eisen,et al.  Research priorities for harnessing plant microbiomes in sustainable agriculture , 2017, PLoS biology.

[24]  Sung-Jin Cho,et al.  Draft genome of the sea cucumber Apostichopus japonicus and genetic polymorphism among color variants , 2017, GigaScience.

[25]  B. Singh,et al.  Microbiome and the future for food and nutrient security , 2017, Microbial biotechnology.

[26]  Xingzhong Liu,et al.  Population Genetics of Hirsutella rhossiliensis, a Dominant Parasite of Cyst Nematode Juveniles on a Continental Scale , 2016, Applied and Environmental Microbiology.

[27]  Jun Wang,et al.  Metagenome-wide association studies: fine-mining the microbiome , 2016, Nature Reviews Microbiology.

[28]  J. Grosser,et al.  Transcriptome analysis of root response to citrus blight based on the newly assembled Swingle citrumelo draft genome , 2016, BMC Genomics.

[29]  P. Schulze-Lefert,et al.  Root Endophyte Colletotrichum tofieldiae Confers Plant Fitness Benefits that Are Phosphate Status Dependent , 2016, Cell.

[30]  Louisa M. Liberman,et al.  Beneficial Microbes Affect Endogenous Mechanisms Controlling Root Development. , 2016, Trends in plant science.

[31]  Brian D. Ondov,et al.  Mash: fast genome and metagenome distance estimation using MinHash , 2015, Genome Biology.

[32]  Alice C. McHardy,et al.  Functional overlap of the Arabidopsis leaf and root microbiota , 2015, Nature.

[33]  Noah Fierer,et al.  Consistent responses of soil microbial communities to elevated nutrient inputs in grasslands across the globe , 2015, Proceedings of the National Academy of Sciences.

[34]  Luis Pedro Coelho,et al.  Structure and function of the global ocean microbiome , 2015, Science.

[35]  P. Bork,et al.  Shotgun metagenomes and multiple primer pair-barcode combinations of amplicons reveal biases in metabarcoding analyses of fungi , 2015 .

[36]  Alice C. McHardy,et al.  Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley , 2015, Cell host & microbe.

[37]  J. Kirkegaard,et al.  Evolution of bacterial communities in the wheat crop rhizosphere. , 2015, Environmental microbiology.

[38]  Cameron Johnson,et al.  Structure, variation, and assembly of the root-associated microbiomes of rice , 2015, Proceedings of the National Academy of Sciences.

[39]  Kunihiko Sadakane,et al.  MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph , 2014, Bioinform..

[40]  J. Setubal,et al.  Announcement of the International Citrus Microbiome (Phytobiome) Consortium. , 2015 .

[41]  Chao Xie,et al.  Fast and sensitive protein alignment using DIAMOND , 2014, Nature Methods.

[42]  Y. Hadar,et al.  Niche and host-associated functional signatures of the root surface microbiome , 2014, Nature Communications.

[43]  Jens Roat Kultima,et al.  An integrated catalog of reference genes in the human gut microbiome , 2014, Nature Biotechnology.

[44]  E. Kuramae,et al.  Taxonomical and functional microbial community selection in soybean rhizosphere , 2014, The ISME Journal.

[45]  Karin M. Fredrikson,et al.  Complex history of admixture during citrus domestication revealed by genome analysis , 2014 .

[46]  Andrea Zuccolo,et al.  Sequencing of diverse mandarin, pummelo and orange genomes reveals complex history of admixture during citrus domestication , 2014, Nature Biotechnology.

[47]  Mikhail S. Gelfand,et al.  Comparative genomics and evolution of regulons of the LacI-family transcription factors , 2014, Front. Microbiol..

[48]  S. Tringe,et al.  Tackling soil diversity with the assembly of large, complex metagenomes , 2014, Proceedings of the National Academy of Sciences.

[49]  B. Singh,et al.  Microbial modulators of soil carbon storage: integrating genomic and metabolic knowledge for global prediction. , 2013, Trends in microbiology.

[50]  Robert C. Edgar,et al.  UPARSE: highly accurate OTU sequences from microbial amplicon reads , 2013, Nature Methods.

[51]  Pelin Yilmaz,et al.  The SILVA ribosomal RNA gene database project: improved data processing and web-based tools , 2012, Nucleic Acids Res..

[52]  Niranjan Nagarajan,et al.  The draft genome of sweet orange (Citrus sinensis) , 2012, Nature Genetics.

[53]  Scott T. Bates,et al.  Cross-biome metagenomic analyses of soil microbial communities and their functional attributes , 2012, Proceedings of the National Academy of Sciences.

[54]  Zhengwei Zhu,et al.  CD-HIT: accelerated for clustering the next-generation sequencing data , 2012, Bioinform..

[55]  R. Amann,et al.  Revealing structure and assembly cues for Arabidopsis root-inhabiting bacterial microbiota , 2012, Nature.

[56]  Robert C. Edgar,et al.  Defining the core Arabidopsis thaliana root microbiome , 2012, Nature.

[57]  C. V. Mering,et al.  Metaproteogenomic analysis of microbial communities in the phyllosphere and rhizosphere of rice , 2011, The ISME Journal.

[58]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[59]  Jizhong Zhou,et al.  Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere , 2011, The ISME Journal.

[60]  In-Jung Lee,et al.  Exophiala sp. LHL08 reprograms Cucumis sativus to higher growth under abiotic stresses. , 2011, Physiologia plantarum.

[61]  Steven Salzberg,et al.  BIOINFORMATICS ORIGINAL PAPER , 2004 .

[62]  E. Uberbacher,et al.  Distinct Microbial Communities within the Endosphere and Rhizosphere of Populus deltoides Roots across Contrasting Soil Types , 2011, Applied and Environmental Microbiology.

[63]  P. Bakker,et al.  Deciphering the Rhizosphere Microbiome for Disease-Suppressive Bacteria , 2011, Science.

[64]  R. Knight,et al.  UniFrac: an effective distance metric for microbial community comparison , 2011, The ISME Journal.

[65]  S. C. Winans,et al.  LuxR‐type quorum‐sensing regulators that are detached from common scents , 2010, Molecular microbiology.

[66]  William A. Walters,et al.  Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample , 2010, Proceedings of the National Academy of Sciences.

[67]  Andy F. S. Taylor,et al.  The UNITE database for molecular identification of fungi--recent updates and future perspectives. , 2010, The New phytologist.

[68]  Miriam L. Land,et al.  Trace: Tennessee Research and Creative Exchange Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification Recommended Citation Prodigal: Prokaryotic Gene Recognition and Translation Initiation Site Identification , 2022 .

[69]  Siu-Ming Yiu,et al.  SOAP2: an improved ultrafast tool for short read alignment , 2009, Bioinform..

[70]  S. Maddocks,et al.  Structure and function of the LysR-type transcriptional regulator (LTTR) family proteins. , 2008, Microbiology.

[71]  F. Gmitter,et al.  The possible role of Yunnan, China, in the origin of contemporary citrus species (rutaceae) , 1990, Economic Botany.

[72]  J. Tiedje,et al.  Naïve Bayesian Classifier for Rapid Assignment of rRNA Sequences into the New Bacterial Taxonomy , 2007, Applied and Environmental Microbiology.

[73]  Alexander F. Auch,et al.  MEGAN analysis of metagenomic data. , 2007, Genome research.

[74]  B. Hillerich,et al.  A New GntR Family Transcriptional Regulator in Streptomyces coelicolor Is Required for Morphogenesis and Antibiotic Production and Controls Transcription of an ABC Transporter in Response to Carbon Source , 2006, Journal of bacteriology.

[75]  J. Ramos,et al.  The IclR family of transcriptional activators and repressors can be defined by a single profile , 2006, Protein science : a publication of the Protein Society.

[76]  C. Alabouvette,et al.  Fusarium oxysporum and its biocontrol. , 2003, The New phytologist.

[77]  A Bairoch,et al.  Arac/XylS family of transcriptional regulators , 1997, Microbiology and molecular biology reviews : MMBR.

[78]  R. Scora,et al.  On the History and Origin of Citrus , 1975 .