Standards in Genomic Sciences最新文献_第3页

A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences. 向生物合成基因簇（MIBiG）最低信息库提交数据的标准化工作流程：基于研究的教育体验前景。

Standards in Genomic Sciences Pub Date : 2018-07-11 DOI: 10.1186/s40793-018-0318-y

Samuel C Epstein, Louise K Charkoudian, Marnix H Medema

{"title":"A standardized workflow for submitting data to the Minimum Information about a Biosynthetic Gene cluster (MIBiG) repository: prospects for research-based educational experiences.","authors":"Samuel C Epstein, Louise K Charkoudian, Marnix H Medema","doi":"10.1186/s40793-018-0318-y","DOIUrl":"10.1186/s40793-018-0318-y","url":null,"abstract":"Microorganisms utilize complex enzymatic pathways to biosynthesize structurally complex and pharmacologically relevant molecules. These pathways are encoded by gene clusters and are found in a diverse set of organisms. The Minimum Information about a Biosynthetic Gene cluster repository facilitates standardized and centralized storage of experimental data on these gene clusters and their molecular products, by utilizing user-submitted data to translate scientific discoveries into a format that can be analyzed computationally. This accelerates the processes of connecting genes to chemical structures, understanding biosynthetic gene clusters in the context of environmental diversity, and performing computer-assisted design of synthetic gene clusters. Here, we present a Standard Operating Procedure, Excel templates, a tutorial video, and a collection of relevant review literature to support scientists in their efforts to submit data into MiBIG. Further, we provide tools to integrate gene cluster annotation projects into the classroom environment, including workflows and assessment materials.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"16"},"PeriodicalIF":0.0,"publicationDate":"2018-07-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-018-0318-y","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36312291","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: 26

Correction to: Complete genome of a novel virulent phage ST0 lysing Escherichia coli H8. 更正:一种新的可裂解大肠杆菌H8的强毒噬菌体ST0的全基因组。

Standards in Genomic Sciences Pub Date : 2018-07-04 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0319-x

Honghui Liu, Xinchun Liu, Jinqing Li

引用次数: 0

Short genome report of cellulose-producing commensal Escherichia coli 1094. 产纤维素共生大肠杆菌1094的短基因组报告。

Standards in Genomic Sciences Pub Date : 2018-05-09 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0316-0

Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier, Jean-Marc Ghigo

引用次数: 2

Complete genome sequence of "Thiodictyon syntrophicum" sp. nov. strain Cad16^T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno. 新菌株 Cad16T 的完整基因组序列，该菌株是从高山兼性湖 Cadagno 分离出来的一种光解自养型紫硫细菌。

Standards in Genomic Sciences Pub Date : 2018-05-09 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0317-z

Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla

{"title":"Complete genome sequence of \"Thiodictyon syntrophicum\" sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.","authors":"Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla","doi":"10.1186/s40793-018-0317-z","DOIUrl":"10.1186/s40793-018-0317-z","url":null,"abstract":"\"Thiodictyon syntrophicum\" sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"14"},"PeriodicalIF":0.0,"publicationDate":"2018-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5944118/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36109272","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

High quality draft genome sequences of Mycoplasma agassizii strains PS6^T and 723 isolated from Gopherus tortoises with upper respiratory tract disease. 上呼吸道疾病地龟阿加西支原体PS6T和723株高质量基因组序列草图

Standards in Genomic Sciences Pub Date : 2018-04-27 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0315-1

David Alvarez-Ponce, Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy

{"title":"High quality draft genome sequences of Mycoplasma agassizii strains PS6T and 723 isolated from Gopherus tortoises with upper respiratory tract disease.","authors":"David Alvarez-Ponce, Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy","doi":"10.1186/s40793-018-0315-1","DOIUrl":"https://doi.org/10.1186/s40793-018-0315-1","url":null,"abstract":"Mycoplasma agassizii is one of the known causative agents of upper respiratory tract disease (URTD) in Mojave desert tortoises (Gopherus agassizii) and in gopher tortoises (Gopherus polyphemus). We sequenced the genomes of M. agassizii strains PS6T (ATCC 700616) and 723 (ATCC 700617) isolated from the upper respiratory tract of a Mojave desert tortoise and a gopher tortoise, respectively, both with signs of URTD. The PS6T genome assembly was organized in eight scaffolds, had a total length of 1,274,972 bp, a G + C content of 28.43%, and contained 979 protein-coding genes, 13 pseudogenes and 35 RNA genes. The 723 genome assembly was organized in 40 scaffolds, had a total length of 1,211,209 bp, a G + C content of 28.34%, and contained 955 protein-coding genes, seven pseudogenes, and 35 RNA genes. Both genomes exhibit a very similar organization and very similar numbers of genes in each functional category. Pairs of orthologous genes encode proteins that are 93.57% identical on average. Homology searches identified a putative cytadhesin. These genomes will enable studies that will help understand the molecular bases of pathogenicity of this and other Mycoplasma species.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"12"},"PeriodicalIF":0.0,"publicationDate":"2018-04-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1186/s40793-018-0315-1","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36068416","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: 4

Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01. 从非产鲸素的 Lividum Janthinobacterium ERGS5:01 的高质量基因组草案中揭示高海拔适应战略。

Standards in Genomic Sciences Pub Date : 2018-04-19 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0313-3

Rakshak Kumar, Vishal Acharya, Dharam Singh, Sanjay Kumar

{"title":"Strategies for high-altitude adaptation revealed from high-quality draft genome of non-violacein producing Janthinobacterium lividum ERGS5:01.","authors":"Rakshak Kumar, Vishal Acharya, Dharam Singh, Sanjay Kumar","doi":"10.1186/s40793-018-0313-3","DOIUrl":"10.1186/s40793-018-0313-3","url":null,"abstract":"A light pink coloured bacterial strain ERGS5:01 isolated from glacial stream water of Sikkim Himalaya was affiliated to Janthinobacterium lividum based on 16S rRNA gene sequence identity and phylogenetic clustering. Whole genome sequencing was performed for the strain to confirm its taxonomy as it lacked the typical violet pigmentation of the genus and also to decipher its survival strategy at the aquatic ecosystem of high elevation. The PacBio RSII sequencing generated genome of 5,168,928 bp with 4575 protein-coding genes and 118 RNA genes. Whole genome-based multilocus sequence analysis clustering, in silico DDH similarity value of 95.1% and, the ANI value of 99.25% established the identity of the strain ERGS5:01 (MCC 2953) as a non-violacein producing J. lividum. The genome comparisons across genus Janthinobacterium revealed an open pan-genome with the scope of the addition of new orthologous cluster to complete the genomic inventory. The genomic insight provided the genetic basis of freezing and frequent freeze-thaw cycle tolerance and, for industrially important enzymes. Extended insight into the genome provided clues of crucial genes associated with adaptation in the harsh aquatic ecosystem of high altitude.","PeriodicalId":21965,"journal":{"name":"Standards in Genomic Sciences","volume":"13 ","pages":"11"},"PeriodicalIF":0.0,"publicationDate":"2018-04-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5909252/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"36064467","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

High-quality draft genome of the methanotroph Methylovulum psychrotolerans Str. HV10-M2 isolated from plant material at a high-altitude environment. 从高海拔植物材料中分离的耐冷甲烷化菌Methylovulum Str. HV10-M2高质量基因组草图。

Standards in Genomic Sciences Pub Date : 2018-04-12 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0314-2

Alejandro Mateos-Rivera, Tajul Islam, Ian P G Marshall, Lars Schreiber, Lise Øvreås

引用次数: 5

High quality draft genome sequence of Mycoplasma testudineum strain BH29^T, isolated from the respiratory tract of a desert tortoise. 从沙漠陆龟呼吸道分离的拉伸支原体BH29T的高质量基因组序列草图。

Standards in Genomic Sciences Pub Date : 2018-04-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0309-z

Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy, David Alvarez-Ponce

引用次数: 4

Genome sequence of Planktotalea frisia type strain (SH6-1^T), a representative of the Roseobacter group isolated from the North Sea during a phytoplankton bloom. 在北海浮游植物繁殖期间分离到的玫瑰杆菌群的代表——弗里西亚浮游菌型菌株(SH6-1T)的基因组序列。

Standards in Genomic Sciences Pub Date : 2018-04-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0311-5

Insa Bakenhus, Sonja Voget, Anja Poehlein, Thorsten Brinkhoff, Rolf Daniel, Meinhard Simon

引用次数: 5

Draft genome sequence of Fermentimonas caenicola strain SIT8, isolated from the human gut. 从人类肠道中分离出的 Fermentimonas caenicola 菌株 SIT8 的基因组序列草案。

Standards in Genomic Sciences Pub Date : 2018-04-11 eCollection Date: 2018-01-01 DOI: 10.1186/s40793-018-0310-6

Mamadou Beye, Sofiane Bakour, Sory Ibrahima Traore, Jaishriram Rathored, Noémie Labas, Didier Raoult, Pierre-Edouard Fournier

引用次数: 0