{"title":"Draft genome sequence of <i>Desulfoplanes formicivorans</i> Pf12B<sup>T</sup>, a sulfate-reducing bacterium of the family <i>Desulfomicrobiaceae</i>.","authors":"Miho Watanabe, Hisaya Kojima, Manabu Fukui","doi":"10.1186/s40793-017-0246-2","DOIUrl":"https://doi.org/10.1186/s40793-017-0246-2","url":null,"abstract":"<p><p><i>Desulfoplanes formicivorans</i> strain Pf12B<sup>T</sup> is the type strain of the type species in the genus <i>Desulfoplanes</i>, which is the one of the genera in the family <i>Desulfomicrobiaceae</i> within the order <i>Desulfovibrionales</i>. This deltaproteobacterium was isolated from a blackish meromictic lake sediment. <i>D. formicivorans</i> strain Pf12B<sup>T</sup> is a Gram-negative, motile and sulfate-reducing bacterium. Cells of strain Pf12B<sup>T</sup> are characterized by possession of vibroid morphology and red fluorescent pigment. Here we describe the features, draft genome sequence and annotation of this organism, the sole species of the genus <i>Desulfoplanes</i>. The genome comprised 3,000,979 bp, 2,657 protein-coding genes and 58 RNA genes.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"34"},"PeriodicalIF":0.0,"publicationDate":"2017-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0246-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35070118","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Shu Harn Te, Boon Fei Tan, Chek Yin Boo, Janelle Renee Thompson, Karina Yew-Hoong Gin
{"title":"Genomics insights into production of 2-methylisoborneol and a putative cyanobactin by <i>Planktothricoides</i> sp. SR001.","authors":"Shu Harn Te, Boon Fei Tan, Chek Yin Boo, Janelle Renee Thompson, Karina Yew-Hoong Gin","doi":"10.1186/s40793-017-0247-1","DOIUrl":"10.1186/s40793-017-0247-1","url":null,"abstract":"<p><p><i>Planktothricoides</i> is a free-living filamentous cyanobacterium belonging to the order Oscillatoriales and the family Phormidiaceae, capable of forming bloom in fresh and brackish waters. A unicyanobacterial non-axenic culture dominated by <i>Planktothricoides</i> sp. SR001 was obtained from a freshwater reservoir in Singapore. The draft genome presented here is the first tropical freshwater <i>Planktothricoides</i> sp. ever sequenced. The genome of 7.0Mbp contains 5,776 genes predicted using the JGI IMG pipeline. The whole genome sequence allows identification of genes encoding for nitrogen-fixation, accessory photosynthetic pigments and biosynthesis of an off-flavor compound, 2-methylisoborneol, which has been experimentally verified here based on metabolite detection. In addition, strain SR001 genome contains an operon putatively involved in the production of a linear tripeptide cyanobactin related to viridisamide A and aeruginosamide, with the later known to possess anti-microbial or cytotoxic effect.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2017-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5460452/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35070119","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Qian Liu, Yue-Hong Wu, Hong Cheng, Lin Xu, Chun-Sheng Wang, Xue-Wei Xu
{"title":"Complete genome sequence of bacteriochlorophyll-synthesizing bacterium <i>Porphyrobacter neustonensis</i> DSM 9434.","authors":"Qian Liu, Yue-Hong Wu, Hong Cheng, Lin Xu, Chun-Sheng Wang, Xue-Wei Xu","doi":"10.1186/s40793-017-0243-5","DOIUrl":"https://doi.org/10.1186/s40793-017-0243-5","url":null,"abstract":"<p><p>The genus <i>Porphyrobacter</i> belongs to aerobic anoxygenic phototrophic bacteria cluster. <i>Porphyrobacter neustonensis</i> DSM 9434 was isolated from a eutrophic freshwater pond in Australia, and is able to synthesize Bacteriochlorophyll <i>a</i> as well as grow under aerobic conditions. It is the type species of the genus <i>Porphyrobacter</i>. Here we describe the characteristics of the strain DSM 9434, including the genome sequence and annotation, synthesis of BChl <i>a</i>, and metabolic pathways of the organism. The genome of strain DSM 9434 comprises 3,090,363 bp and contains 2,902 protein-coding genes, 47 tRNA genes and 6 rRNA genes. Strain DSM 9434 encodes 46 genes which participate in BChl <i>a</i> synthesis and this investigation shed light on the evolution and functional implications regarding bacteriochlorophyll synthesis.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2017-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0243-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34988982","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Steffen L Jørgensen, Egle Kudirkiene, Lili Li, Jens P Christensen, John E Olsen, Lisa Nolan, Rikke H Olsen
{"title":"Chromosomal features of <i>Escherichia coli</i> serotype O2:K2, an avian pathogenic <i>E. coli</i>.","authors":"Steffen L Jørgensen, Egle Kudirkiene, Lili Li, Jens P Christensen, John E Olsen, Lisa Nolan, Rikke H Olsen","doi":"10.1186/s40793-017-0245-3","DOIUrl":"https://doi.org/10.1186/s40793-017-0245-3","url":null,"abstract":"<p><p><i>Escherichia coli</i> causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic <i>E. coli.</i> Avian pathogenic <i>E. coli</i> is a subgroup of extra-intestinal pathogenic <i>E. coli</i> and infections due to avian pathogenic <i>E. coli</i> have major impact on poultry production economy and welfare worldwide. An almost defining characteristic of avian pathogenic <i>E. coli</i> is the carriage of plasmids, which may encode virulence factors and antibiotic resistance determinates. For the same reason, plasmids of avian pathogenic <i>E. coli</i> have been intensively studied. However, genes encoded by the chromosome may also be important for disease manifestation and antimicrobial resistance. For the <i>E. coli</i> strain APEC_O2 the plasmids have been sequenced and analyzed in several studies, and <i>E. coli</i> APEC_O2 may therefore serve as a reference strain in future studies. Here we describe the chromosomal features of <i>E. coli</i> APEC_O2. <i>E. coli</i> APEC_O2 is a sequence type ST135, has a chromosome of 4,908,820 bp (plasmid removed), comprising 4672 protein-coding genes, 110 RNA genes, and 156 pseudogenes, with an average G + C content of 50.69%. We identified 82 insertion sequences as well as 4672 protein coding sequences, 12 predicated genomic islands, three prophage-related sequences, and two clustered regularly interspaced short palindromic repeats regions on the chromosome, suggesting the possible occurrence of horizontal gene transfer in this strain. The wildtype strain of <i>E. coli</i> APEC_O2 is resistant towards multiple antimicrobials, however, no (complete) antibiotic resistance genes were present on the chromosome, but a number of genes associated with extra-intestinal disease were identified. Together, the information provided here on <i>E. coli</i> APEC_O2 will assist in future studies of avian pathogenic <i>E. coli</i> strains, in particular regarding strain of <i>E. coli</i> APEC_O2, and aid in the general understanding of the pathogenesis of avian pathogenic <i>E. coli</i>.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"33"},"PeriodicalIF":0.0,"publicationDate":"2017-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0245-3","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34988983","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Sivan Laviad-Shitrit, Markus Göker, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides, Malka Halpern
{"title":"High quality permanent draft genome sequence of <i>Chryseobacterium bovis</i> DSM 19482<sup>T</sup>, isolated from raw cow milk.","authors":"Sivan Laviad-Shitrit, Markus Göker, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Chris Daum, Nicole Shapiro, Victor Markowitz, Natalia Ivanova, Tanja Woyke, Hans-Peter Klenk, Nikos C Kyrpides, Malka Halpern","doi":"10.1186/s40793-017-0242-6","DOIUrl":"https://doi.org/10.1186/s40793-017-0242-6","url":null,"abstract":"<p><p><i>Chryseobacterium bovis</i> DSM 19482<sup>T</sup> (Hantsis-Zacharov et al., Int J Syst Evol Microbiol 58:1024-1028, 2008) is a Gram-negative, rod shaped, non-motile, facultative anaerobe, chemoorganotroph bacterium. <i>C. bovis</i> is a member of the <i>Flavobacteriaceae</i>, a family within the phylum <i>Bacteroidetes</i>. It was isolated when psychrotolerant bacterial communities in raw milk and their proteolytic and lipolytic traits were studied. Here we describe the features of this organism, together with the draft genome sequence and annotation. The DNA G + C content is 38.19%. The chromosome length is 3,346,045 bp. It encodes 3236 proteins and 105 RNA genes. The <i>C. bovis</i> genome is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes study.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2017-05-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0242-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34983751","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Vanessa Jag, Anja Poehlein, Frank R Bengelsdorf, Rolf Daniel, Peter Dürre
{"title":"Genome sequencing and description of <i>Oerskovia enterophila</i> VJag, an agar- and cellulose-degrading bacterium.","authors":"Vanessa Jag, Anja Poehlein, Frank R Bengelsdorf, Rolf Daniel, Peter Dürre","doi":"10.1186/s40793-017-0244-4","DOIUrl":"https://doi.org/10.1186/s40793-017-0244-4","url":null,"abstract":"<p><p>A nonmotile, Gram-positive bacterium that shows an elongated and branching cell shape was isolated from soil samples from the botanical garden of Ulm University, Ulm, Germany. Here, the isolation procedure, identification, genome sequencing and metabolic features of the strain are described. Phylogenetic analysis allowed to identify the isolated strain as <i>Oerskovia enterophila.</i> The genus <i>Oerskovia</i> belongs to the family <i>Cellulomonadaceae</i> within the order <i>Actinomycetales</i>. The length of cells of <i>O. enterophila</i> ranges from 1 μm to 15 μm, depending on the growth phase. In the exponential growth phase, cells show an elongated and branching shape, whereas cells break up to round or coccoid elements in the stationary growth phase. The 4,535,074 bp long genome consists of 85 contigs with 3918 protein-coding genes and 57 RNA genes. The isolated strain was shown to degrade numerous complex carbon sources such as cellulose, chitin, and starch, which can be found ubiquitously in nature. Moreover, analysis of the genomic sequence revealed the genetic potential to degrade these compounds.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2017-05-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0244-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34978259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu, Alberto P Macho
{"title":"Genome sequencing and analysis of <i>Ralstonia solanacearum</i> phylotype I strains FJAT-91, FJAT-452 and FJAT-462 isolated from tomato, eggplant, and chili pepper in China.","authors":"Yidan Sun, Keke Wang, Carlos Caceres-Moreno, Wei Jia, Aojun Chen, Heng Zhang, Renyi Liu, Alberto P Macho","doi":"10.1186/s40793-017-0241-7","DOIUrl":"10.1186/s40793-017-0241-7","url":null,"abstract":"<p><p><i>Ralstonia solanacearum</i> is an extremely destructive pathogen able to cause disease in a wide range of host plants. Here we report the draft genome sequences of the strains FJAT-91, FJAT-452 and FJAT-462, isolated from tomato, eggplant, and chili pepper, respectively, in China. In addition to the genome annotation, we performed a search for type-III secreted effectors in these strains, providing a detailed annotation of their presence and distinctive features compared to the effector repertoire of the reference phylotype I strain (GMI1000). In this analysis, we found that each strain has a unique effector repertoire, encoding both strain-specific effector variants and variations shared among all three strains. Our study, based on strains isolated from different hosts within the same geographical location, provides insight into effector repertoires sufficient to cause disease in different hosts, and may contribute to the identification of host specificity determinants for <i>R. solanacearum</i>.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"2017-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5393021/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34929740","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Complete genome sequence of <i>Kosakonia oryzae</i> type strain Ola 51<sup>T</sup>.","authors":"Yuanyuan Li, Shuying Li, Mingyue Chen, Guixiang Peng, Zhiyuan Tan, Qianli An","doi":"10.1186/s40793-017-0240-8","DOIUrl":"10.1186/s40793-017-0240-8","url":null,"abstract":"<p><p>Strain Ola 51<sup>T</sup> (=LMG 24251<sup>T</sup> = CGMCC 1.7012<sup>T</sup>) is the type strain of the species <i>Kosakonia oryzae</i> and was isolated from surface-sterilized roots of the wild rice species <i>Oryza latifolia</i> grown in Guangdong, China. Here we summarize the features of the strain Ola 51<sup>T</sup> and describe its complete genome sequence. The genome contains one circular chromosome of 5,303,342 nucleotides with 54.01% GC content, 4773 protein-coding genes, 16 rRNA genes, 76 tRNA genes, 13 ncRNA genes, 48 pseudo genes, and 1 CRISPR array.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2017-04-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0240-8","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34929739","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, Bart C Weimer
{"title":"Automation of PacBio SMRTbell NGS library preparation for bacterial genome sequencing.","authors":"Nguyet Kong, Whitney Ng, Kao Thao, Regina Agulto, Allison Weis, Kristi Spittle Kim, Jonas Korlach, Luke Hickey, Lenore Kelly, Stephen Lappin, Bart C Weimer","doi":"10.1186/s40793-017-0239-1","DOIUrl":"https://doi.org/10.1186/s40793-017-0239-1","url":null,"abstract":"<p><strong>Background: </strong>The PacBio RS II provides for single molecule, real-time DNA technology to sequence genomes and detect DNA modifications. The starting point for high-quality sequence production is high molecular weight genomic DNA. To automate the library preparation process, there must be high-throughput methods in place to assess the genomic DNA, to ensure the size and amounts of the sheared DNA fragments and final library.</p><p><strong>Findings: </strong>The library construction automation was accomplished using the Agilent NGS workstation with Bravo accessories for heating, shaking, cooling, and magnetic bead manipulations for template purification. The quality control methods from gDNA input to final library using the Agilent Bioanalyzer System and Agilent TapeStation System were evaluated.</p><p><strong>Conclusions: </strong>Automated protocols of PacBio 10 kb library preparation produced libraries with similar technical performance to those generated manually. The TapeStation System proved to be a reliable method that could be used in a 96-well plate format to QC the DNA equivalent to the standard Bioanalyzer System results. The DNA Integrity Number that is calculated in the TapeStation System software upon analysis of genomic DNA is quite helpful to assure that the starting genomic DNA is not degraded. In this respect, the gDNA assay on the TapeStation System is preferable to the DNA 12000 assay on the Bioanalyzer System, which cannot run genomic DNA, nor can the Bioanalyzer work directly from the 96-well plates.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2017-03-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0239-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34858149","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Wayne Reeve, Peter van Berkum, Julie Ardley, Rui Tian, Margaret Gollagher, Dora Marinova, Patrick Elia, T B K Reddy, Manoj Pillay, Neha Varghese, Rekha Seshadri, Natalia Ivanova, Tanja Woyke, Mohamed N Baeshen, Nabih A Baeshen, Nikos Kyrpides
{"title":"High-quality permanent draft genome sequence of the <i>Bradyrhizobium elkanii</i> type strain USDA 76<sup>T</sup>, isolated from <i>Glycine max</i> (L.) Merr.","authors":"Wayne Reeve, Peter van Berkum, Julie Ardley, Rui Tian, Margaret Gollagher, Dora Marinova, Patrick Elia, T B K Reddy, Manoj Pillay, Neha Varghese, Rekha Seshadri, Natalia Ivanova, Tanja Woyke, Mohamed N Baeshen, Nabih A Baeshen, Nikos Kyrpides","doi":"10.1186/s40793-017-0238-2","DOIUrl":"https://doi.org/10.1186/s40793-017-0238-2","url":null,"abstract":"<p><p><i>Bradyrhizobium elkanii</i> USDA 76<sup>T</sup> (INSCD = ARAG00000000), the type strain for <i>Bradyrhizobium elkanii</i>, is an aerobic, motile, Gram-negative, non-spore-forming rod that was isolated from an effective nitrogen-fixing root nodule of <i>Glycine max</i> (L. Merr) grown in the USA. Because of its significance as a microsymbiont of this economically important legume, <i>B. elkanii</i> USDA 76<sup>T</sup> was selected as part of the DOE Joint Genome Institute 2010 <i>Genomic Encyclopedia for Bacteria and Archaea-Root Nodule Bacteria</i> sequencing project. Here the symbiotic abilities of <i>B. elkanii</i> USDA 76<sup>T</sup> are described, together with its genome sequence information and annotation. The 9,484,767 bp high-quality draft genome is arranged in 2 scaffolds of 25 contigs, containing 9060 protein-coding genes and 91 RNA-only encoding genes. The <i>B. elkanii</i> USDA 76<sup>T</sup> genome contains a low GC content region with symbiotic <i>nod</i> and <i>fix</i> genes, indicating the presence of a symbiotic island integration. A comparison of five <i>B. elkanii</i> genomes that formed a clique revealed that 356 of the 9060 protein coding genes of USDA 76<sup>T</sup> were unique, including 22 genes of an intact resident prophage. A conserved set of 7556 genes were also identified for this species, including genes encoding a general secretion pathway as well as type II, III, IV and VI secretion system proteins. The type III secretion system has previously been characterized as a host determinant for <i>Rj</i> and/or <i>rj</i> soybean cultivars. Here we show that the USDA 76<sup>T</sup> genome contains genes encoding all the type III secretion system components, including a translocon complex protein NopX required for the introduction of effector proteins into host cells. While many bradyrhizobial strains are unable to nodulate the soybean cultivar Clark (<i>rj1</i>), USDA 76<sup>T</sup> was able to elicit nodules on Clark (<i>rj1</i>), although in reduced numbers, when plants were grown in Leonard jars containing sand or vermiculite. In these conditions, we postulate that the presence of NopX allows USDA 76<sup>T</sup> to introduce various effector molecules into this host to enable nodulation.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"26"},"PeriodicalIF":0.0,"publicationDate":"2017-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0238-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34792006","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}