Standards in Genomic Sciences最新文献_第9页

The complete genome sequence of the cold adapted crude-oil degrader: Pedobacter steynii DX4. 适应寒冷环境的原油降解菌的完整基因组序列：Steynii DX4 杆菌的完整基因组序列。

Standards in Genomic Sciences Pub Date : 2017-07-27 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0249-z

Sijing Chang, Gaosen Zhang, Ximing Chen, Haozhi Long, Yilin Wang, Tuo Chen, Guangxiu Liu

引用次数: 0

Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436^T. 沙地放线菌dodonnocardioides FR1436T全基因组序列。

Standards in Genomic Sciences Pub Date : 2017-07-25 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0257-z

Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim

{"title":"Complete genome sequence of the sand-sediment actinobacterium Nocardioides dokdonensis FR1436T.","authors":"Min-Jung Kwak, Soon-Kyeong Kwon, Jihyun F Kim","doi":"10.1186/s40793-017-0257-z","DOIUrl":"https://doi.org/10.1186/s40793-017-0257-z","url":null,"abstract":"Nocardioides dokdonensis, belonging to the class Actinobacteria, was first isolated from sand sediment of a beach in Dokdo, Korea, in 2005. In this study, we determined the genome sequence of FR1436, the type strain of N. dokdonensis, and analyzed its gene contents. The genome sequence is the second complete one in the genus Nocardioides after that of Nocardioides sp. JS614. It is composed of a 4,376,707-bp chromosome with a G + C content of 72.26%. From the genome sequence, 4,104 CDSs, three rRNA operons, 51 tRNAs, and one tmRNA were predicted, and 71.38% of the genes were assigned putative functions. Through the sequence analysis, dozens of genes involved in steroid metabolism, especially its degradation, were detected. Most of the identified genes were located in large gene clusters, which showed high similarities with the gene clusters in Pimelobacter simplex VKM Ac-2033D. Genomic features of N. dokdonensis associated with steroid catabolism indicate that it could be used for research and application of steroids in science and industry.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"44"},"PeriodicalIF":0.0,"publicationDate":"2017-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0257-z","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35238960","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: 2

First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile. 从智利北部Ascotán盐湖分离的fususibacter属菌株的基因组序列初稿。

Standards in Genomic Sciences Pub Date : 2017-07-24 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0252-4

Antonio E Serrano, Lorena V Escudero, Cinthya Tebes-Cayo, Mauricio Acosta, Olga Encalada, Sebastián Fernández-Moroso, Cecilia Demergasso

{"title":"First draft genome sequence of a strain from the genus Fusibacter isolated from Salar de Ascotán in Northern Chile.","authors":"Antonio E Serrano, Lorena V Escudero, Cinthya Tebes-Cayo, Mauricio Acosta, Olga Encalada, Sebastián Fernández-Moroso, Cecilia Demergasso","doi":"10.1186/s40793-017-0252-4","DOIUrl":"https://doi.org/10.1186/s40793-017-0252-4","url":null,"abstract":"Fusibacter sp. 3D3 (ATCC BAA-2418) is an arsenate-reducing halotolerant strain within the Firmicutes phylum, isolated from the Salar de Ascotán, a hypersaline salt flat in Northern Chile. This high-Andean closed basin is an athalassohaline environment located at the bottom of a tectonic basin surrounded by mountain range, including some active volcanoes. This landscape can be an advantageous system to explore the effect of salinity on microorganisms that mediate biogeochemical reactions. Since 2000, microbial reduction of arsenic has been evidenced in the system, and the phylogenetic analysis of the original community plus the culture enrichments has revealed the predominance of Firmicutes phylum. Here, we describe the first whole draft genome sequence of an arsenic-reducing strain belonging to the Fusibacter genus showing the highest 16S rRNA gene sequence similarity (98%) with Fusibacter sp. strain Vns02. The draft genome consists of 57 contigs with 5,111,250 bp and an average G + C content of 37.6%. Out of 4780 total genes predicted, 4700 genes code for proteins and 80 genes for RNAs. Insights from the genome sequence and some microbiological features of the strain 3D3 are available under Bioproject accession PRJDB4973 and Biosample SAMD00055724. The release of the genome sequence of this strain could contribute to the understanding of the arsenic biogeochemistry in extreme environments.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"43"},"PeriodicalIF":0.0,"publicationDate":"2017-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0252-4","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35238959","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: 23

Neisseria lactamica Y92-1009 complete genome sequence. 内酰胺奈瑟菌Y92-1009全基因组序列。

Standards in Genomic Sciences Pub Date : 2017-07-24 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0250-6

Anish K Pandey, David W Cleary, Jay R Laver, Martin C J Maiden, Xavier Didelot, Andrew Gorringe, Robert C Read

{"title":"Neisseria lactamica Y92-1009 complete genome sequence.","authors":"Anish K Pandey, David W Cleary, Jay R Laver, Martin C J Maiden, Xavier Didelot, Andrew Gorringe, Robert C Read","doi":"10.1186/s40793-017-0250-6","DOIUrl":"https://doi.org/10.1186/s40793-017-0250-6","url":null,"abstract":"We present the high quality, complete genome assembly of Neisseria lactamica Y92-1009 used to manufacture an outer membrane vesicle (OMV)-based vaccine, and a member of the Neisseria genus. The strain is available on request from the Public Health England Meningococcal Reference Unit. This Gram negative, dipplococcoid bacterium is an organism of worldwide clinical interest because human nasopharyngeal carriage is related inversely to the incidence of meningococcal disease, caused by Neisseria meningitidis. The organism sequenced was isolated during a school carriage survey in Northern Ireland in 1992 and has been the subject of a variety of laboratory and clinical studies. Four SMRT cells on a RSII machine by Pacific Biosystems were used to produce a complete, closed genome assembly. Sequence data were obtained for a total of 30,180,391 bases from 2621 reads and assembled using the HGAP algorithm. The assembly was corrected using short reads obtained from an Illumina HiSeq 2000instrument. This resulted in a 2,146,723 bp assembly with approximately 460 fold mean coverage depth and a GC ratio of 52.3%.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"41"},"PeriodicalIF":0.0,"publicationDate":"2017-07-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0250-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35238956","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

The genome of the cotton bacterial blight pathogen Xanthomonas citri pv. malvacearum strain MSCT1. 棉花白叶枯病菌柑橘黄单胞菌的基因组分析。乳突菌MSCT1。

Standards in Genomic Sciences Pub Date : 2017-07-24 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0253-3

Kurt C Showmaker, Mark A Arick, Chuan-Yu Hsu, Brigitte E Martin, Xiaoqiang Wang, Jiayuan Jia, Martin J Wubben, Robert L Nichols, Tom W Allen, Daniel G Peterson, Shi-En Lu

引用次数: 6

Insights into Cedecea neteri strain M006 through complete genome sequence, a rare bacterium from aquatic environment. 通过对水生环境中罕见细菌Cedecea neteri菌株M006的全基因组测序研究。

Standards in Genomic Sciences Pub Date : 2017-07-21 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0255-1

Kok-Gan Chan, Wen-Si Tan

引用次数: 7

Draft genome sequences of strains Salinicola socius SMB35^T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia. 绘制俄罗斯Verkhnekamsk钾肥矿区产盐杆菌SMB35T、盐杆菌sp. MH3R3-1和盐杆菌sp. SMB17的基因组序列。

Standards in Genomic Sciences Pub Date : 2017-07-19 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0251-5

Björn E Olsson, Ekaterina S Korsakova, Lyudmila N Anan'ina, Anna A Pyankova, Olga V Mavrodi, Elena G Plotnikova, Dmitri V Mavrodi

{"title":"Draft genome sequences of strains Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17 from the Verkhnekamsk potash mining region of Russia.","authors":"Björn E Olsson, Ekaterina S Korsakova, Lyudmila N Anan'ina, Anna A Pyankova, Olga V Mavrodi, Elena G Plotnikova, Dmitri V Mavrodi","doi":"10.1186/s40793-017-0251-5","DOIUrl":"https://doi.org/10.1186/s40793-017-0251-5","url":null,"abstract":"Halomonads are moderately halophilic bacteria that are studied as models of prokaryotic osmoadaptation and sources of enzymes and chemicals for biotechnological applications. Despite the progress in understanding the diversity of these organisms, our ability to explain ecological, metabolic, and biochemical traits of halomonads at the genomic sequence level remains limited. This study addresses this gap by presenting draft genomes of Salinicola socius SMB35T, Salinicola sp. MH3R3-1 and Chromohalobacter sp. SMB17, which were isolated from potash mine tailings in the Verkhnekamsk salt deposit area of Russia. The analysis of these genomes confirmed the importance of ectoines and quaternary amines to the capacity of halomonads to tolerate osmotic stress and adapt to hypersaline environments. The study also revealed that Chromohalobacter and Salinicola share 75-90% of the predicted proteome, but also harbor a set of genus-specific genes, which in Salinicola amounted to approximately 0.5 Mbp. These genus-specific genome segments may contribute to the phenotypic diversity of the Halomonadaceae and the ability of these organisms to adapt to changing environmental conditions and colonize new ecological niches.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"39"},"PeriodicalIF":0.0,"publicationDate":"2017-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0251-5","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35188966","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: 10

High-quality draft genome sequence of a biofilm forming lignocellulolytic Aspergillus niger strain ATCC 10864. 形成木质纤维素水解黑曲霉菌株ATCC 10864生物膜的高质量基因组序列草图。

Standards in Genomic Sciences Pub Date : 2017-07-17 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0254-2

Sujay Paul, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa

{"title":"High-quality draft genome sequence of a biofilm forming lignocellulolytic Aspergillus niger strain ATCC 10864.","authors":"Sujay Paul, Yvette Ludeña, Gretty K Villena, Fengan Yu, David H Sherman, Marcel Gutiérrez-Correa","doi":"10.1186/s40793-017-0254-2","DOIUrl":"https://doi.org/10.1186/s40793-017-0254-2","url":null,"abstract":"Filamentous fungus Aspergillus niger has high industrial value due to their lignocellulolytic enzyme activities and ATCC 10864 is one of the few type strains of A. niger which has a unique biofilm forming capability. Here we report the first draft genome sequence of A. niger ATCC 10864 strain. The genome of A. niger ATCC 10864 is 36,172,237 bp long and comprise of 310 scaffolds with 49.5% average GC content. A total of 10,804 protein-coding genes were predicted among which 10,761 genes were with putative functions. A. niger ATCC 10864 genome coded for 709 putative carbohydrate active enzyme families distributed in six functional categories and among them glycoside hydrolases (GHs) represent the most number of families (279). Genes that include pepA, brlA, exgA, LaeA, rodA, GCN have also been identified in this study, which may play a role in biofilm formation. This high-quality draft genome sequence will facilitate our understanding of the mechanisms behind fungal biofilm formation and higher lignocellulolytic enzyme production.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"37"},"PeriodicalIF":0.0,"publicationDate":"2017-07-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0254-2","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35184874","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: 10

Complete genome sequence of Leuconostoc suionicum DSM 20241^T provides insights into its functional and metabolic features. suionicum Leuconostoc DSM 20241T全基因组测序为其功能和代谢特征提供了新的见解。

Standards in Genomic Sciences Pub Date : 2017-07-17 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0256-0

Byung Hee Chun, Se Hee Lee, Hye Hee Jeon, Dong-Woon Kim, Che Ok Jeon

引用次数: 10

Complete genome sequence of Microbulbifer sp. CCB-MM1, a halophile isolated from Matang Mangrove Forest, Malaysia. 马来西亚马唐红树林嗜盐菌Microbulbifer sp. CCB-MM1的全基因组序列

Standards in Genomic Sciences Pub Date : 2017-07-06 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0248-0

Tsu Horng Moh, Nyok-Sean Lau, Go Furusawa, Al-Ashraf Abdullah Amirul

引用次数: 12