Standards in Genomic Sciences最新文献

{"title":"Complete genome of Rhizobium <i>leguminosarum</i> Norway, an ineffective <i>Lotus</i> micro-symbiont.","authors":"Juan Liang,&nbsp;Anne Hoffrichter,&nbsp;Andreas Brachmann,&nbsp;Macarena Marín","doi":"10.1186/s40793-018-0336-9","DOIUrl":"https://doi.org/10.1186/s40793-018-0336-9","url":null,"abstract":"<p><p>Rhizobia bacteria engage in nitrogen-fixing root nodule symbiosis, a mutualistic interaction with legume plants in which a bidirectional nutrient exchange takes place. Occasionally, this interaction is suboptimal resulting in the formation of ineffective nodules in which little or no atmospheric nitrogen fixation occurs. <i>Rhizobium leguminosarum</i> Norway induces ineffective nodules in a wide range of <i>Lotus</i> hosts. To investigate the basis of this phenotype, we sequenced the complete genome of <i>Rl</i> Norway and compared it to the genome of the closely related strain <i>R. leguminosarum</i> bv. <i>viciae</i> 3841. The genome comprises 7,788,085 bp, distributed on a circular chromosome containing 63% of the genomic information and five large circular plasmids. The functionally classified bacterial gene set is distributed evenly among all replicons. All symbiotic genes (<i>nod</i>, <i>fix</i>, <i>nif</i>) are located on the pRLN3 plasmid. Whole genome comparisons revealed differences in the metabolic repertoire and in protein secretion systems, but not in classical symbiotic genes.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"36"},"PeriodicalIF":0.0,"publicationDate":"2018-12-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-018-0336-9","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36757761","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":"Draft genomes of <i>Cronobacter sakazakii</i> strains isolated from dried spices bring unique insights into the diversity of plant-associated strains.","authors":"Hyein Jang,&nbsp;Jungha Woo,&nbsp;Youyoung Lee,&nbsp;Flavia Negrete,&nbsp;Samantha Finkelstein,&nbsp;Hannah R Chase,&nbsp;Nicole Addy,&nbsp;Laura Ewing,&nbsp;Junia Jean Gilles Beaubrun,&nbsp;Isha Patel,&nbsp;Jayanthi Gangiredla,&nbsp;Athmanya Eshwar,&nbsp;Ziad W Jaradat,&nbsp;Kunho Seo,&nbsp;Srikumar Shabarinath,&nbsp;Séamus Fanning,&nbsp;Roger Stephan,&nbsp;Angelika Lehner,&nbsp;Ben D Tall,&nbsp;Gopal R Gopinath","doi":"10.1186/s40793-018-0339-6","DOIUrl":"10.1186/s40793-018-0339-6","url":null,"abstract":"<p><p><i>Cronobacter sakazakii</i> is a Gram-negative opportunistic pathogen that causes life- threatening infantile infections, such as meningitis, septicemia, and necrotizing enterocolitis, as well as pneumonia, septicemia, and urinary tract and wound infections in adults. Here, we report 26 draft genome sequences of <i>C. sakazakii</i>, which were obtained from dried spices from the USA, the Middle East, China, and the Republic of Korea. The average genome size of the <i>C. sakazakii</i> genomes was 4393 kb, with an average of 4055 protein coding genes, and an average genome G + C content of 56.9%. The genomes contained genes related to carbohydrate transport and metabolism, amino acid transport and metabolism, and cell wall/membrane biogenesis. In addition, we identified genes encoding proteins involved in osmotic responses such as DnaJ, Aquaproin Z, ProQ, and TreF, as well as virulence-related and heat shock-related proteins. Interestingly, a metabolic island comprised of a variably-sized xylose utilization operon was found within the spice-associated <i>C. sakazakii</i> genomes, which supports the hypothesis that plants may serve as transmission vectors or alternative hosts for <i>Cronobacter</i> species. The presence of the genes identified in this study can support the remarkable phenotypic traits of <i>C. sakazakii</i> such as the organism's capabilities of adaptation and survival in response to adverse growth environmental conditions (e.g. osmotic and desiccative stresses). Accordingly, the genome analyses provided insights into many aspects of physiology and evolutionary history of this important foodborne pathogen.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"35"},"PeriodicalIF":0.0,"publicationDate":"2018-11-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-018-0339-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36744655","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":"High-quality-draft genome sequence of the heavy metal resistant and exopolysaccharides producing bacterium <i>Mucilaginibacter pedocola</i> TBZ30^T.","authors":"Xia Fan, Jingwei Tang, Li Nie, Jing Huang, Gejiao Wang","doi":"10.1186/s40793-018-0337-8","DOIUrl":"10.1186/s40793-018-0337-8","url":null,"abstract":"<p><p><i>Mucilaginibacter pedocola</i> TBZ30^T (= CCTCC AB 2015301^T = KCTC 42833^T) is a Gram- negative, rod-shaped, non-motile and non-spore-forming bacterium isolated from a heavy metal contaminated paddy field. It shows resistance to multiple heavy metals and can adsorb/remove Zn²⁺ and Cd²⁺ during cultivation. In addition, strain TBZ30^T produces exopolysaccharides (EPS). These features make it a great potential to bioremediate heavy metal contamination and biotechnical application. Here we describe the genome sequence and annotation of strain TBZ30^T. The genome size is 7,035,113 bp, contains 3132 protein-coding genes (2736 with predicted functions), 50 tRNA encoding genes and 14 rRNA encoding genes. Putative heavy metal resistant genes and EPS associated genes are found in the genome.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"34"},"PeriodicalIF":0.0,"publicationDate":"2018-11-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6260751/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36741870","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>Arcticibacterium luteifluviistationis</i> SM1504^T, a cytophagaceae bacterium isolated from Arctic surface seawater.","authors":"Yi Li, Xiao-Han Guo, Yan-Ru Dang, Lin-Lin Sun, Xi-Ying Zhang, Xiu-Lan Chen, Qi-Long Qin, Peng Wang","doi":"10.1186/s40793-018-0335-x","DOIUrl":"10.1186/s40793-018-0335-x","url":null,"abstract":"<p><p><i>Arcticibacterium luteifluviistationis</i> SM1504^T was isolated from Arctic surface seawater and classified as a novel genus of the phylum <i>Bacteroides</i>. To date, no <i>Arcticibacterium</i> genomes have been reported, their genomic compositions and metabolic features are still unknown. Here, we reported the complete genome sequence of <i>A. luteifluviistationis</i> SM1504^T, which comprises 5,379,839 bp with an average GC content of 37.20%. Genes related to various stress (such as radiation, osmosis and antibiotics) resistance and gene clusters coding for carotenoid and flexirubin biosynthesis were detected in the genome. Moreover, the genome contained a 245-kb genomic island and a 15-kb incomplete prophage region. A great percentage of proteins belonging to carbohydrate metabolism especially in regard to polysaccharides utilization were found. These related genes and metabolic characteristics revealed genetic basis for adapting to the diverse extreme Arctic environments. The genome sequence of <i>A. luteifluviistationis</i> SM1504^T also implied that the genus <i>Arcticibacterium</i> may act as a vital organic carbon matter decomposer in the Arctic seawater ecosystem.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"33"},"PeriodicalIF":0.0,"publicationDate":"2018-11-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6258284/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36741982","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":"The draft genome sequence of \"<i>Nitrospira lenta</i>\" strain BS10, a nitrite oxidizing bacterium isolated from activated sludge.","authors":"Dimitra Sakoula, Boris Nowka, Eva Spieck, Holger Daims, Sebastian Lücker","doi":"10.1186/s40793-018-0338-7","DOIUrl":"10.1186/s40793-018-0338-7","url":null,"abstract":"<p><p>The genus <i>Nitrospira</i> is considered to be the most widespread and abundant group of nitrite-oxidizing bacteria in many natural and man-made ecosystems. However, the ecophysiological versatility within this phylogenetic group remains highly understudied, mainly due to the lack of pure cultures and genomic data. To further expand our understanding of this biotechnologically important genus, we analyzed the high quality draft genome of \"<i>Nitrospira lenta</i>\" strain BS10, a sublineage II <i>Nitrospira</i> that was isolated from a municipal wastewater treatment plant in Hamburg, Germany. The genome of \"<i>N. lenta</i>\" has a size of 3,756,190 bp and contains 3968 genomic objects, of which 3907 are predicted protein-coding sequences. Thorough genome annotation allowed the reconstruction of the \"<i>N. lenta</i>\" core metabolism for energy conservation and carbon fixation. Comparative analyses indicated that most metabolic features are shared with <i>N. moscoviensis</i> and \"<i>N. defluvii</i>\", despite their ecological niche differentiation and phylogenetic distance. In conclusion, the genome of \"<i>N. lenta</i>\" provides important insights into the genomic diversity of the genus <i>Nitrospira</i> and provides a foundation for future comparative genomic studies that will generate a better understanding of the nitrification process.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"32"},"PeriodicalIF":0.0,"publicationDate":"2018-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6251164/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36782423","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>Planococcus</i> sp. PAMC21323 isolated from Antarctica and its metabolic potential to detoxify pollutants.","authors":"Jong-Hyun Jung, Min-Ho Joe, Dong-Ho Kim, Hyun Park, Jong-Il Choi, Sangyong Lim","doi":"10.1186/s40793-018-0334-y","DOIUrl":"10.1186/s40793-018-0334-y","url":null,"abstract":"<p><p>The <i>Planococcus</i> sp. PAMC21323 is a yellow pigment-producing bacterium isolated from King George Island in Antarctica; it has a broad growth temperature range of 5-40 °C. Herein, we describe the complete genome sequence information of the genus <i>Planococcus</i> with its annotated sequence, genetic features for bioremediation, and oxidative stress capacity. The <i>Planococcus</i> sp. PAMC21323 possesses chromosomal DNA (3,196,500-bp) with plasmid DNA (3364-bp). The complete 3,199,864-bp of the genome consists of 3171 genes including 60 transfer RNAs and 24 ribosomal RNAs. Strain PAMC21323 encodes various genes associated with detoxification of heavy metal ions and aromatic hydrocarbons. Moreover, it is equipped with diverse stress response systems, which can be used to sense the internal and oxidative stresses caused by detoxification. This is the first report highlighting the genetic potential of <i>Planococcus</i> sp. PAMC21323 in bioremediation, suggesting application of this psychrotrophic strain in bioremediation in harsh environments.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"31"},"PeriodicalIF":0.0,"publicationDate":"2018-11-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6225704/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36699688","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":"Draft genome sequence of <i>Bacillus amyloliquefaciens</i> subsp. <i>plantarum</i> strain Fito_F321, an endophyte microorganism from <i>Vitis vinifera</i> with biocontrol potential.","authors":"Cátia Pinto, Susana Sousa, Hugo Froufe, Conceição Egas, Christophe Clément, Florence Fontaine, Ana C Gomes","doi":"10.1186/s40793-018-0327-x","DOIUrl":"10.1186/s40793-018-0327-x","url":null,"abstract":"<p><p><i>Bacillus amyloliquefaciens subsp. plantarum</i> strain Fito_F321 is a naturally occurring strain in vineyard, with the ability to colonise grapevine and which unveils a naturally antagonistic potential against phytopathogens of grapevine, including those responsible for the <i>Botryosphaeria</i> dieback, a GTD disease. Herein we report the draft genome sequence of <i>B. amyloliquefaciens</i> subsp. <i>plantarum</i> Fito_F321, isolated from the leaf of <i>Vitis vinifera</i> cv. Merlot at Bairrada appellation (Cantanhede, Portugal). The genome size is 3,856,229 bp, with a GC content of 46.54% that contains 3697 protein-coding genes, 86 tRNA coding genes and 5 rRNA genes. The draft genome of strain Fito_F321 allowed to predict a set of bioactive compounds as bacillaene, difficidin, macrolactin, surfactin and fengycin that due to their antimicrobial activity are hypothesized to be of utmost importance for biocontrol of grapevine diseases.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"30"},"PeriodicalIF":0.0,"publicationDate":"2018-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211603/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36707768","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":"High-quality-draft genome sequence of the multiple heavy metal resistant bacterium <i>Pseudaminobacter manganicus</i> JH-7^T.","authors":"Xian Xia, Jiahong Li, Zijie Zhou, Dan Wang, Jing Huang, Gejiao Wang","doi":"10.1186/s40793-018-0330-2","DOIUrl":"10.1186/s40793-018-0330-2","url":null,"abstract":"<p><p><i>Pseudaminobacter manganicus</i> JH-7^T (= KCTC 52258^T = CCTCC AB 2016107^T) is a Gram-staining-negative, aerobic and non-motile strain that was isolated from a manganese mine<i>.</i> The strain JH-7^T shows multiple heavy metal resistance and can effectively remove Mn²⁺ and Cd²⁺. In addition, it is able to produce exopolysaccharides (EPS), which may contribute to metal remove/adsorption. Thus, strain JH-7^T shows a great potential in bioremediation of heavy metal-contaminated environment. In this study, we report the draft genomic sequence of <i>P. manganicus</i> JH-7^T and compare it to related genomes. Strain JH-7^T has a 4,842,937 bp genome size with a G + C content of 61.2%, containing 4504 protein-coding genes and 71 RNA genes. A large number of putative genes associated with heavy metal resistance and EPS synthesis are found in the genome.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"29"},"PeriodicalIF":0.0,"publicationDate":"2018-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6203287/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36628313","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 the nitrogen-fixing bacterium <i>Azospirillum humicireducens</i> type strain SgZ-5^T.","authors":"Zhen Yu, Guiqin Yang, Xiaoming Liu, Yueqiang Wang, Li Zhuang, Shungui Zhou","doi":"10.1186/s40793-018-0322-2","DOIUrl":"10.1186/s40793-018-0322-2","url":null,"abstract":"<p><p>The <i>Azospirillum humicireducens</i> strain SgZ-5^T, belonging to the Order <i>Rhodospirillales</i> and the Family <i>Rhodospirillaceae</i>, was isolated from a microbial fuel cell inoculated with paddy soil. A previous work has shown that strain SgZ-5^T was able to fix atmospheric nitrogen involved in plant growth promotion. Here we present the complete genome of <i>A. humicireducens</i> SgZ-5^T, which consists of a circular chromosome and six plasmids with the total genome size of 6,834,379 bp and the average GC content of 67.55%. Genome annotations predicted 5969 protein coding and 85 RNA genes including 14 rRNA and 67 tRNA genes. By genomic analysis, we identified a complete set of genes that is potentially involved in nitrogen fixation and its regulation. This genome also harbors numerous genes that are likely responsible for phytohormones production. We anticipate that the <i>A. humicireducens</i> SgZ-5^T genome will contribute insights into plant growth promoting properties of <i>Azospirillum</i> strains.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2018-10-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6192227/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36597932","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":"Draft genomes of \"<i>Pectobacterium peruviense</i>\" strains isolated from fresh water in France.","authors":"Pierre Faye, Claire Bertrand, Jacques Pédron, Marie-Anne Barny","doi":"10.1186/s40793-018-0332-0","DOIUrl":"10.1186/s40793-018-0332-0","url":null,"abstract":"<p><p>Bacteria belonging to the genus <i>Pectobacterium</i> are responsible for soft rot disease on a wide range of cultivated crops. The \"<i>Pectobacterium peruviense</i>\" specie, recently proposed inside the <i>Pectobacterium</i> genus, gathers strains isolated from potato tubers cultivated in Peru at high altitude. Here we report the draft genome sequence of two strains belonging to \"<i>P. peruviense</i>\" isolated from river water in France indicating that the geographic distribution of this specie is likely to be larger than previously anticipated. We compared these genomes with the one published from the \"<i>P. peruviense</i>\" specie type strain isolated in Peru.</p>","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"27"},"PeriodicalIF":0.0,"publicationDate":"2018-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36604254","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}