Standards in Genomic Sciences最新文献_第2页

Draft genome sequences of Cylindrospermopsis raciborskii strains CS-508 and MVCC14, isolated from freshwater bloom events in Australia and Uruguay. 从澳大利亚和乌拉圭的淡水水华事件中分离出的Cylindrosperopsis raciborskii菌株CS-508和MVCC14的基因组序列草案。

Standards in Genomic Sciences Pub Date : 2018-10-12 DOI: 10.1186/s40793-018-0323-1

Juan J Fuentes-Valdés, Katia Soto-Liebe, Danilo Pérez-Pantoja, Javier Tamames, Lucy Belmar, Carlos Pedrós-Alió, Daniel Garrido, Mónica Vásquez

引用次数: 4

Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications. Chloroflexales order 的候选代表--"Candidatus Chloroploca asiatica "和 "Candidatus Viridilinea mediisalina "的基因组序列草案：系统发育和分类学意义。

Standards in Genomic Sciences Pub Date : 2018-10-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0329-8

Denis S Grouzdev, Maria S Rysina, Irina A Bryantseva, Vladimir M Gorlenko, Vasil A Gaisin

{"title":"Draft genome sequences of 'Candidatus Chloroploca asiatica' and 'Candidatus Viridilinea mediisalina', candidate representatives of the Chloroflexales order: phylogenetic and taxonomic implications.","authors":"Denis S Grouzdev, Maria S Rysina, Irina A Bryantseva, Vladimir M Gorlenko, Vasil A Gaisin","doi":"10.1186/s40793-018-0329-8","DOIUrl":"10.1186/s40793-018-0329-8","url":null,"abstract":"'Candidatus Chloroploca asiatica' B7-9 and 'Candidatus Viridilinea mediisalina' Kir15-3F are mesophilic filamentous anoxygenic phototrophic bacteria from alkaline aquatic environments. Both bacteria became available in the last few years and only in stable enrichment culture. In this study, we report the draft genomic sequences of 'Ca. Chloroploca asiatica' B7-9 and 'Ca. Viridilinea mediisalina' Kir15-3F, which were assembled from metagenomes of their cultures with a fold coverage 86.3× and 163.8×, respectively. The B7-9 (5.8 Mb) and the Kir15-3F (5.6 Mb) draft genome harbors 4818 and 4595 predicted protein-coding genes, respectively. In this article, we analyzed the phylogeny of representatives of the Chloroflexineae suborder in view of the appearance of new genomic data. These data were used for the revision of earlier published group-specific conserved signature indels and for searching for novel signatures for taxons in the Chloroflexineae suborder.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"24"},"PeriodicalIF":0.0,"publicationDate":"2018-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180586/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36598649","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}

引用次数: 0

Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough. 从阿尔及利亚土壤油泥中分离的苏云金芽孢杆菌DNG9生物活性物质基因组序列草案的见解。

Standards in Genomic Sciences Pub Date : 2018-10-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0331-1

Mohamed Seghir Daas, Albert Remus R Rosana, Jeella Z Acedo, Malika Douzane, Farida Nateche, Salima Kebbouche-Gana, John C Vederas

{"title":"Insights into the draft genome sequence of bioactives-producing Bacillus thuringiensis DNG9 isolated from Algerian soil-oil slough.","authors":"Mohamed Seghir Daas, Albert Remus R Rosana, Jeella Z Acedo, Malika Douzane, Farida Nateche, Salima Kebbouche-Gana, John C Vederas","doi":"10.1186/s40793-018-0331-1","DOIUrl":"10.1186/s40793-018-0331-1","url":null,"abstract":"Bacillus thuringiensis is widely used as a bioinsecticide due to its ability to form parasporal crystals containing proteinaceous toxins. It is a member of the Bacillus cereus sensu lato, a group with low genetic diversity but produces several promising antimicrobial compounds. B. thuringiensis DNG9, isolated from an oil-contaminated slough in Algeria, has strong antibacterial, antifungal and biosurfactant properties. Here, we report the 6.06 Mbp draft genome sequence of B. thuringiensis DNG9. The genome encodes several gene inventories for the biosynthesis of bioactive compounds such as zwittermycin A, petrobactin, insecticidal toxins, polyhydroxyalkanoates and multiple bacteriocins. We expect the genome information of strain DNG9 will provide another model system to study pathogenicity against insect pests, plant diseases, and antimicrobial compound mining and comparative phylogenesis among the Bacillus cereus sensu lato group.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"25"},"PeriodicalIF":0.0,"publicationDate":"2018-10-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6186030/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36604252","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}

引用次数: 0

First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico. 墨西哥假结核棒状杆菌菌株的首次基因组测序和比较分析。

Standards in Genomic Sciences Pub Date : 2018-10-10 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0325-z

Doglas Parise, Mariana T D Parise, Marcus V C Viana, Adrian V Muñoz-Bucio, Yazmin A Cortés-Pérez, Beatriz Arellano-Reynoso, Efrén Díaz-Aparicio, Fernanda A Dorella, Felipe L Pereira, Alex F Carvalho, Henrique C P Figueiredo, Preetam Ghosh, Debmalya Barh, Anne C P Gomide, Vasco A C Azevedo

{"title":"First genome sequencing and comparative analyses of Corynebacterium pseudotuberculosis strains from Mexico.","authors":"Doglas Parise, Mariana T D Parise, Marcus V C Viana, Adrian V Muñoz-Bucio, Yazmin A Cortés-Pérez, Beatriz Arellano-Reynoso, Efrén Díaz-Aparicio, Fernanda A Dorella, Felipe L Pereira, Alex F Carvalho, Henrique C P Figueiredo, Preetam Ghosh, Debmalya Barh, Anne C P Gomide, Vasco A C Azevedo","doi":"10.1186/s40793-018-0325-z","DOIUrl":"10.1186/s40793-018-0325-z","url":null,"abstract":"Corynebacterium pseudotuberculosis is a pathogenic bacterium which has been rapidly spreading all over the world, causing economic losses in the agricultural sector and sporadically infecting humans. Six C. pseudotuberculosis strains were isolated from goats, sheep, and horses with distinct abscess locations. For the first time, Mexican genomes of this bacterium were sequenced and studied in silico. All strains were sequenced using Ion Personal Genome Machine sequencer, assembled using Newbler and SPAdes software. The automatic genome annotation was done using the software RAST and in-house scripts for transference, followed by manual curation using Artemis software and BLAST against NCBI and UniProt databases. The six genomes are publicly available in NCBI database. The analysis of nucleotide sequence similarity and the generated phylogenetic tree led to the observation that the Mexican strains are more similar between strains from the same host, but the genetic structure is probably more influenced by transportation of animals between farms than host preference. Also, a putative drug target was predicted and in silico analysis of 46 strains showed two gene clusters capable of differentiating the biovars equi and ovis: Restriction Modification system and CRISPR-Cas cluster.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"21"},"PeriodicalIF":0.0,"publicationDate":"2018-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36598646","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}

引用次数: 0

The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil. 从原油污染土壤中分离出的新型耐寒细菌 Planococcus maritimus Y42 的完整基因组序列。

Standards in Genomic Sciences Pub Date : 2018-10-10 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0328-9

Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang, Sijing Chang

{"title":"The complete genomic sequence of a novel cold-adapted bacterium, Planococcus maritimus Y42, isolated from crude oil-contaminated soil.","authors":"Ruiqi Yang, Guangxiu Liu, Tuo Chen, Wei Zhang, Gaosen Zhang, Sijing Chang","doi":"10.1186/s40793-018-0328-9","DOIUrl":"10.1186/s40793-018-0328-9","url":null,"abstract":"Planococcus maritimus Y42, isolated from the petroleum-contaminated soil of the Qaidam Basin, can use crude oil as its sole source of carbon and energy at 20 °C. The genome of P. maritimus strain Y42 has been sequenced to provide information on its properties. Genomic analysis shows that the genome of strain Y42 contains one circular DNA chromosome with a size of 3,718,896 bp and a GC content of 48.8%, and three plasmids (329,482; 89,073; and 12,282 bp). Although the strain Y42 did not show a remarkably higher ability in degrading crude oil than other oil-degrading bacteria, the existence of strain Y42 played a significant role to reducing the overall environmental impact as an indigenous oil-degrading bacterium. In addition, genome annotation revealed that strain Y42 has many genes responsible for hydrocarbon degradation. Structural features of the genomes might provide a competitive edge for P. maritimus strain Y42 to survive in oil-polluted environments and be worthy of further study in oil degradation for the recovery of crude oil-polluted environments.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"23"},"PeriodicalIF":0.0,"publicationDate":"2018-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6180392/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36598648","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}

引用次数: 0

One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070. 四个热相Brochothrix菌株CD 337、TAP 175、BSAS1 3和EBP 3070的一个完整的和三个基因组草图序列。

Standards in Genomic Sciences Pub Date : 2018-10-10 DOI: 10.1186/s40793-018-0333-z

Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, Emmanuel Jaffrès, Monique Zagorec

{"title":"One complete and three draft genome sequences of four Brochothrix thermosphacta strains, CD 337, TAP 175, BSAS1 3 and EBP 3070.","authors":"Nassima Illikoud, Christophe Klopp, Alain Roulet, Olivier Bouchez, Nathalie Marsaud, Emmanuel Jaffrès, Monique Zagorec","doi":"10.1186/s40793-018-0333-z","DOIUrl":"10.1186/s40793-018-0333-z","url":null,"abstract":"Brochothrix thermosphacta is one of the dominant bacterial species associated with spoilage of chilled meat and seafood products through the production of various metabolites responsible for off-odors. However, metabolic pathways leading to meat and seafood spoilage are not all well known. The production of spoiling molecules seems to depend both on strains and on food matrix. Several B. thermosphacta genome sequences have been reported, all issued from meat isolates. Here, we report four genome sequences, one complete and three as drafts. The four B. thermosphacta strains CD 337, TAP 175, BSAS1 3, and EBP 3070 were isolated from different ecological niches (seafood or meat products either spoiled or not and bovine slaughterhouse). These strains known as phenotypically and genetically different were selected to represent intraspecies diversity. CD 337 genome is 2,594,337 bp long, complete and circular, containing 2593 protein coding sequences and 28 RNA genes. TAP 175, BSAS1 3, and EBP 3070 genomes are arranged in 57, 83, and 71 contigs, containing 2515, 2668, and 2611 protein-coding sequences, respectively. These genomes were compared with two other B. thermosphacta complete genome sequences. The main genome content differences between strains are phages, plasmids, restriction/modification systems, and cell surface functions, suggesting a similar metabolic potential but a different niche adaptation capacity.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"22"},"PeriodicalIF":0.0,"publicationDate":"2018-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-018-0333-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36598647","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}

引用次数: 6

Functional and taxonomic classification of a greenhouse water drain metagenome. 温室排水宏基因组的功能与分类。

Standards in Genomic Sciences Pub Date : 2018-10-05 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0326-y

Gamaliel López-Leal, Fernanda Cornejo-Granados, Juan Manuel Hurtado-Ramírez, Alfredo Mendoza-Vargas, Adrian Ochoa-Leyva

引用次数: 3

Complete genome sequence of the halophile bacterium Kushneria konosiri X49^T, isolated from salt-fermented Konosirus punctatus. 嗜盐细菌Kushneria konosiri X49T的全基因组序列，该细菌是从盐发酵的点状孔藻中分离的。

Standards in Genomic Sciences Pub Date : 2018-10-01 DOI: 10.1186/s40793-018-0324-0

Ji-Hyun Yun, Hojun Sung, Hyun Sik Kim, Euon Jung Tak, Woorim Kang, June-Young Lee, Dong-Wook Hyun, Pil Soo Kim, Jin-Woo Bae

引用次数: 7

Complete genome sequence of the Robinia pseudoacacia L. symbiont Mesorhizobium amorphae CCNWGS0123. 刺槐共生体无定形中根菌CCNWGS0123全基因组序列

Standards in Genomic Sciences Pub Date : 2018-09-18 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0321-3

Xinye Wang, Yantao Luo, Dongying Liu, Jiamei Wang, Shi Wei, Liang Zhao

引用次数: 7

Correction to: Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE). 更正：生物网络计算建模第四次会议的会议报告。

Standards in Genomic Sciences Pub Date : 2018-08-09 DOI: 10.1186/s40793-018-0320-4

Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Michael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet

引用次数: 11