Standards in Genomic Sciences最新文献_第4页

Draft genome sequence of Bosea sp. WAO an arsenite and sulfide oxidizer isolated from a pyrite rock outcrop in New Jersey. 从新泽西州黄铁矿露头中分离出的亚砷酸盐和硫化物氧化剂Bosea sp. WAO的基因组序列草图。

Standards in Genomic Sciences Pub Date : 2018-04-10 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0312-4

Alexandra B Walczak, Nathan Yee, Lily Y Young

引用次数: 5

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

Standards in Genomic Sciences Pub Date : 2018-02-16 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-017-0288-5

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

引用次数: 2

Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants. 假单胞菌alcaliphila JAB1 (=DSM 26533)的全基因组序列。

Standards in Genomic Sciences Pub Date : 2018-02-01 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-017-0306-7

Jakub Ridl, Jachym Suman, Serena Fraraccio, Miluse Hradilova, Michal Strejcek, Tomas Cajthaml, Andrea Zubrova, Tomas Macek, Hynek Strnad, Ondrej Uhlik

{"title":"Complete genome sequence of Pseudomonas alcaliphila JAB1 (=DSM 26533), a versatile degrader of organic pollutants.","authors":"Jakub Ridl, Jachym Suman, Serena Fraraccio, Miluse Hradilova, Michal Strejcek, Tomas Cajthaml, Andrea Zubrova, Tomas Macek, Hynek Strnad, Ondrej Uhlik","doi":"10.1186/s40793-017-0306-7","DOIUrl":"https://doi.org/10.1186/s40793-017-0306-7","url":null,"abstract":"In this study, following its isolation from contaminated soil, the genomic sequence of Pseudomonas alcaliphila strain JAB1 (=DSM 26533), a biphenyl-degrading bacterium, is reported and analyzed in relation to its extensive degradative capabilities. The P. alcaliphila JAB1 genome (GenBank accession no. CP016162) consists of a single 5.34 Mbp-long chromosome with a GC content of 62.5%. Gene function was assigned to 3816 of the 4908 predicted genes. The genome harbors a bph gene cluster, permitting degradation of biphenyl and many congeners of polychlorinated biphenyls (PCBs), a ben gene cluster, enabling benzoate and its derivatives to be degraded, and phe gene cluster, which permits phenol degradation. In addition, P. alcaliphila JAB1 is capable of cometabolically degrading cis-1,2-dichloroethylene (cDCE) when grown on phenol. The strain carries both catechol and protocatechuate branches of the β-ketoadipate pathway, which is used to funnel the pollutants to the central metabolism. Furthermore, we propose that clustering of MALDI-TOF MS spectra with closest phylogenetic relatives should be used when taxonomically classifying the isolated bacterium; this, together with 16S rRNA gene sequence and chemotaxonomic data analyses, enables more precise identification of the culture at the species level.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"3"},"PeriodicalIF":0.0,"publicationDate":"2018-02-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0306-7","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35822889","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: 32

Draft genome sequence of Streptomyces hyaluromycini MB-PO13^T, a hyaluromycin producer. 绘制透明霉素产生物透明霉素链霉菌MB-PO13T的基因组序列。

Standards in Genomic Sciences Pub Date : 2018-01-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-017-0286-7

Enjuro Harunari, Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Akane Kimura, Moriyuki Hamada, Yasuhiro Igarashi

引用次数: 3

Genomic insights into Mycobacterium simiae human colonization. 猿猴分枝杆菌人类定植的基因组学启示。

Standards in Genomic Sciences Pub Date : 2018-01-08 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-017-0291-x

José L Steffani-Vallejo, Marion E Brunck, Erika Y Acosta-Cruz, Rafael Montiel, Francisco Barona-Gómez

{"title":"Genomic insights into Mycobacterium simiae human colonization.","authors":"José L Steffani-Vallejo, Marion E Brunck, Erika Y Acosta-Cruz, Rafael Montiel, Francisco Barona-Gómez","doi":"10.1186/s40793-017-0291-x","DOIUrl":"10.1186/s40793-017-0291-x","url":null,"abstract":"Mycobacterium simiae (Karassova V, Weissfeiler J, Kraszanay E, Acta Microbiol Acad Sci Hung 12:275-82, 1965) is a slow-growing nontuberculous Mycobacterium species found in environmental niches, and recently evidenced as an opportunistic Human pathogen. We report here the genome of a clinical isolate of M. simiae (MsiGto) obtained from a patient in Guanajuato, Mexico. With a size of 6,684,413 bp, the genomic sequence of strain MsiGto is the largest of the three M. simiae genomes reported to date. Gene prediction revealed 6409 CDSs in total, including 6354 protein-coding genes and 52 RNA genes. Comparative genomic analysis identified shared features between strain MsiGto and the other two reported M. simiae genomes, as well as unique genes. Our data reveals that M. simiae MsiGto harbors virulence-related genes, such as arcD, ESAT-6, and those belonging to the antigen 85 complex and mce clusters, which may explain its successful transition to the human host. We expect the genome information of strain MsiGto will provide a better understanding of infective mechanisms and virulence of this emergent pathogen.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"1"},"PeriodicalIF":0.0,"publicationDate":"2018-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5759803/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35741995","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

Genome sequence of Acuticoccus yangtzensis JL1095T (DSM 28604T) isolated from the Yangtze Estuary. 长江口扬子急性球菌JL1095T (DSM 28604T)基因组序列分析

Standards in Genomic Sciences Pub Date : 2017-12-29 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0295-6

Lei Hou, Jia Sun, Xiabing Xie, Nianzhi Jiao, Yao Zhang

引用次数: 4

Genome of Russian wheat aphid an economically important cereal aphid. 经济上重要的谷类蚜虫——俄罗斯小麦蚜虫的基因组。

Standards in Genomic Sciences Pub Date : 2017-12-28 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0307-6

Nicolaas Francois Visser Burger, Anna-Maria Botha

{"title":"Genome of Russian wheat aphid an economically important cereal aphid.","authors":"Nicolaas Francois Visser Burger, Anna-Maria Botha","doi":"10.1186/s40793-017-0307-6","DOIUrl":"https://doi.org/10.1186/s40793-017-0307-6","url":null,"abstract":"Although the hemipterans (Aphididae) are comprised of roughly 50,000 extant insect species, only four have sequenced genomes that are publically available, namely Acyrthosiphon pisum (pea aphid), Rhodnius prolixus (Kissing bug), Myzus persicae (Green peach aphid) and Diuraphis noxia (Russian wheat aphid). As a significant proportion of agricultural pests are phloem feeding aphids, it is crucial for sustained global food security that a greater understanding of the genomic and molecular functioning of this family be elucidated. Recently, the genome of US D. noxia biotype US2 was sequenced but its assembly only incorporated ~ 32% of produced reads and contained a surprisingly low gene count when compared to that of the model/first sequenced aphid, A. pisum. To this end, we present here the genomes of two South African Diuraphis noxia (Kurdjumov, Hemiptera: Aphididae) biotypes (SA1 and SAM), obtained after sequencing the genomes of the only two D. noxia biotypes with documented linked genealogy. To better understand overall targets and patterns of heterozygosity, we also sequenced a pooled sample of 9 geographically separated D. noxia populations (MixIX). We assembled a 399 Mb reference genome (PRJNA297165, representing 64% of the projected genome size 623 Mb) using ± 28 Gb of 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SAM, whilst ± 13 Gb 101 bp paired-end HiSeq2000 reads from the D. noxia biotype SA1 were generated to facilitate genomic comparisons between the two biotypes. Sequencing the MixIX sample yielded ±26 Gb 50 bp paired-end SOLiD reads which facilitated SNP detection when compared to the D. noxia biotype SAM assembly. Ab initio gene calling produced a total of 31,885 protein coding genes from the assembled contigs spanning ~ 399 Mb (GCA_001465515.1).","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"90"},"PeriodicalIF":0.0,"publicationDate":"2017-12-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0307-6","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35706996","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: 18

The draft genome of Brucella abortus strain Ba col-B012, isolated from a dairy farm in Nariño, Colombia, bring new insights into the epidemiology of biovar 4 strains. 从哥伦比亚Nariño的一个奶牛场分离到的流产布鲁氏菌菌株Ba col-B012的基因组草图为生物多样性4菌株的流行病学提供了新的见解。

Standards in Genomic Sciences Pub Date : 2017-12-22 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0299-2

Mauricio Pacheco-Montealegre, Rocío E Patiño, Ligia Torres, Sabrina Jiménez, José Luis Rodríguez, Alejandro Caro-Quintero

引用次数: 3

Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9^T. 产酯酶细菌海洋Croceicoccus marinus E4A9T全基因组序列。

Standards in Genomic Sciences Pub Date : 2017-12-21 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0300-0

Yue-Hong Wu, Hong Cheng, Ying-Yi Huo, Lin Xu, Qian Liu, Chun-Sheng Wang, Xue-Wei Xu

{"title":"Complete genome sequence of esterase-producing bacterium Croceicoccus marinus E4A9T.","authors":"Yue-Hong Wu, Hong Cheng, Ying-Yi Huo, Lin Xu, Qian Liu, Chun-Sheng Wang, Xue-Wei Xu","doi":"10.1186/s40793-017-0300-0","DOIUrl":"https://doi.org/10.1186/s40793-017-0300-0","url":null,"abstract":"Croceicoccus marinus E4A9Twas isolated from deep-sea sediment collected from the East Pacific polymetallic nodule area. The strain is able to produce esterase, which is widely used in the food, perfume, cosmetic, chemical, agricultural and pharmaceutical industries. Here we describe the characteristics of strain E4A9, including the genome sequence and annotation, presence of esterases, and metabolic pathways of the organism. The genome of strain E4A9T comprises 4,109,188 bp, with one chromosome (3,001,363 bp) and two large circular plasmids (761,621 bp and 346,204 bp, respectively). Complete genome contains 3653 coding sequences, 48 tRNAs, two operons of 16S-23S-5S rRNA gene and three ncRNAs. Strain E4A9T encodes 10 genes related to esterase, and three of the esterases (E3, E6 and E10) was successfully cloned and expressed in Escherichia coli Rosetta in a soluble form, revealing its potential application in biotechnological industry. Moreover, the genome provides clues of metabolic pathways of strain E4A9T, reflecting its adaptations to the ambient environment. The genome sequence of C. marinus E4A9T now provides the fundamental information for future studies.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"88"},"PeriodicalIF":0.0,"publicationDate":"2017-12-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0300-0","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35706963","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: 3

Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565^T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring. salsuginis Dethiosulfovibrio DSM 21565T的基因组序列草图，这是一种从哥伦比亚咸水泉分离出来的厌氧、轻度嗜盐细菌。

Standards in Genomic Sciences Pub Date : 2017-12-20 eCollection Date: 2017-01-01 DOI: 10.1186/s40793-017-0303-x

Carolina Díaz-Cárdenas, Gina López, José David Alzate-Ocampo, Laura N González, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Silvia Restrepo, Sandra Baena

{"title":"Draft genome sequence of Dethiosulfovibrio salsuginis DSM 21565T an anaerobic, slightly halophilic bacterium isolated from a Colombian saline spring.","authors":"Carolina Díaz-Cárdenas, Gina López, José David Alzate-Ocampo, Laura N González, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Silvia Restrepo, Sandra Baena","doi":"10.1186/s40793-017-0303-x","DOIUrl":"https://doi.org/10.1186/s40793-017-0303-x","url":null,"abstract":"A bacterium belonging to the phylum Synergistetes, genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T (DSM 21565T= KCTC 5659T) is a mesophilic, strictly anaerobic, slightly halophilic, Gram negative bacterium with a diderm cell envelope. The strain ferments peptides, amino acids and a few organic acids. Here we present the description of the complete genome sequencing and annotation of the type species Dethiosulfovibrio salsuginis USBA 82T. The genome consisted of 2.68 Mbp with a 53.7% G + C. A total of 2609 genes were predicted and of those, 2543 were protein coding genes and 66 were RNA genes. We detected in USBA 82T genome six Synergistetes conserved signature indels (CSIs), specific for Jonquetella, Pyramidobacter and Dethiosulfovibrio. The genome of D. salsuginis contained, as expected, genes related to amino acid transport, amino acid metabolism and thiosulfate reduction. These genes represent the major gene groups of Synergistetes, related with their phenotypic traits, and interestingly, 11.8% of the genes in the genome belonged to the amino acid fermentation COG category. In addition, we identified in the genome some ammonification genes such as nitrate reductase genes. The presence of proline operon genes could be related to de novo synthesis of proline to protect the cell in response to high osmolarity. Our bioinformatics workflow included antiSMASH and BAGEL3 which allowed us to identify bacteriocins genes in the genome.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"12 ","pages":"86"},"PeriodicalIF":0.0,"publicationDate":"2017-12-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-017-0303-x","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35687107","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