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Standards in Genomic Sciences

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https://www.readbyqxmd.com/read/29774086/complete-genome-sequence-of-thiodictyon-syntrophicum-sp-nov-strain-cad16-t-a-photolithoautotrophic-purple-sulfur-bacterium-isolated-from-the-alpine-meromictic-lake-cadagno
#1
Samuel M Luedin, Joël F Pothier, Francesco Danza, Nicola Storelli, Niels-Ulrik Frigaard, Matthias Wittwer, Mauro Tonolla
" 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...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29760866/short-genome-report-of-cellulose-producing-commensal-escherichia-coli-1094
#2
Joaquin Bernal-Bayard, Laura Gomez-Valero, Aimee Wessel, Varun Khanna, Christiane Bouchier, Jean-Marc Ghigo
Bacterial surface colonization and biofilm formation often rely on the production of an extracellular polymeric matrix that mediates cell-cell and cell-surface contacts. In Escherichia coli and many Betaproteobacteria and Gammaproteobacteria cellulose is often the main component of the extracellular matrix. Here we report the complete genome sequence of the cellulose producing strain E. coli 1094 and compare it with five other closely related genomes within E. coli phylogenetic group A. We present a comparative analysis of the regions encoding genes responsible for cellulose biosynthesis and discuss the changes that could have led to the loss of this important adaptive advantage in several E...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29725499/high-quality-draft-genome-sequences-of-mycoplasma-agassizii-strains-ps6-t-and-723-isolated-from-gopherus-tortoises-with-upper-respiratory-tract-disease
#3
David Alvarez-Ponce, Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy
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...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29721151/strategies-for-high-altitude-adaptation-revealed-from-high-quality-draft-genome-of-non-violacein-producing-janthinobacterium-lividum-ergs5-01
#4
Rakshak Kumar, Vishal Acharya, Dharam Singh, Sanjay Kumar
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...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29686747/high-quality-draft-genome-of-the-methanotroph-methylovulum-psychrotolerans-str-hv10-m2-isolated-from-plant-material-at-a-high-altitude-environment
#5
Alejandro Mateos-Rivera, Tajul Islam, Ian P G Marshall, Lars Schreiber, Lise Øvreås
Here we present the genome of Methylovulum psychrotolerans strain HV10-M2, a methanotroph isolated from Hardangervidda national park (Norway). This strain represents the second of the two validly published species genus with a sequenced genome. The other is M. miyakonense HT12, which is the type strain of the species and the type species of the genus Methylovulum. We present the genome of M. psychrotolerants str. HV10-M2 and discuss the differences between M. psychrotolerans and M. miyakonense . The genome size of M...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682170/high-quality-draft-genome-sequence-of-mycoplasma-testudineum-strain-bh29-t-isolated-from-the-respiratory-tract-of-a-desert-tortoise
#6
Chava L Weitzman, Richard L Tillett, Franziska C Sandmeier, C Richard Tracy, David Alvarez-Ponce
Mycoplasma testudineum is one of the pathogens that can cause upper respiratory tract disease in desert tortoises, Gopherus agassizii . We sequenced the genome of M. testudineum BH29T (ATCC 700618T  = MCCM 03231T ), isolated from the upper respiratory tract of a Mojave desert tortoise with upper respiratory tract disease. The sequenced draft genome, organized in 25 scaffolds, has a length of 960,895 bp and a G + C content of 27.54%. A total of 788 protein-coding sequences, six pseudogenes and 35 RNA genes were identified...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682169/draft-genome-sequence-of-fermentimonas-caenicola-strain-sit8-isolated-from-the-human-gut
#7
Mamadou Beye, Sofiane Bakour, Sory Ibrahima Traore, Jaishriram Rathored, Noémie Labas, Didier Raoult, Pierre-Edouard Fournier
We report the properties of a draft genome sequence of the bacterium Fermentimonas caenicola strain SIT8 (= CSUR P1560). This strain, whose genome is described here, was isolated from the fecal flora of a healthy 28-month-old Senegalese boy. Strain SIT8 is a facultatively anaerobic Gram-negative bacillus. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,824,451-bp long (1 chromosome but no plasmid) contains 2354 protein-coding and 46 RNA genes, including four rRNA genes...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682168/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
#8
Insa Bakenhus, Sonja Voget, Anja Poehlein, Thorsten Brinkhoff, Rolf Daniel, Meinhard Simon
Planktotalea frisia SH6-1T Hahnke et al. (Int J Syst Evol Microbiol 62:1619-24, 2012) is a planktonic marine bacterium isolated during a phytoplankton bloom from the southern North Sea. It belongs to the Roseobacter group within the alphaproteobacterial family Rhodobacteraceae . Here we describe the draft genome sequence and annotation of the type strain SH6-1T . The genome comprises 4,106,736 bp and contains 4128 protein-coding and 38 RNA genes. The draft genome sequence provides evidence for at least three extrachromosomal elements, encodes genes for DMSP utilization, quorum sensing, photoheterotrophy and a type IV secretion system...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29682167/draft-genome-sequence-of-bosea-sp-wao-an-arsenite-and-sulfide-oxidizer-isolated-from-a-pyrite-rock-outcrop-in-new-jersey
#9
Alexandra B Walczak, Nathan Yee, Lily Y Young
This genome report describes the draft genome and physiological characteristics of Bosea sp. WAO (=DSM 102914), a novel strain of the genus Bosea in the family Bradyrhizobiaceae . Bosea sp. WAO was isolated from pulverized pyritic shale containing elevated levels of arsenic. This aerobic, gram negative microorganism is capable of facultative chemolithoautotrophic growth under aerobic conditions by oxidizing the electron donors arsenite, elemental sulfur, thiosulfate, polysulfide, and amorphous sulfur. The draft genome is of a single circular chromosome 6,125,776 bp long consisting of 21 scaffolds with a G + C content of 66...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29467915/correction-to-neisseria-lactamica-y92-1009-complete-genome-sequence
#10
Anish K Pandey, David W Cleary, Jay R Laver, Martin C J Maiden, Xavier Didelot, Andrew Gorringe, Robert C Read
[This corrects the article DOI: 10.1186/s40793-017-0250-6.].
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29435100/complete-genome-sequence-of-pseudomonas-alcaliphila-jab1-dsm-26533-a-versatile-degrader-of-organic-pollutants
#11
Jakub Ridl, Jachym Suman, Serena Fraraccio, Miluse Hradilova, Michal Strejcek, Tomas Cajthaml, Andrea Zubrova, Tomas Macek, Hynek Strnad, Ondrej Uhlik
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...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29371910/draft-genome-sequence-of-streptomyces-hyaluromycini-mb-po13-t-a-hyaluromycin-producer
#12
Enjuro Harunari, Hisayuki Komaki, Natsuko Ichikawa, Akira Hosoyama, Akane Kimura, Moriyuki Hamada, Yasuhiro Igarashi
Streptomyces hyaluromycini MB-PO13T (=NBRC 110483T  = DSM 100105T ) is type strain of the species, which produces a hyaluronidase inhibitor, hyaluromycin. Here, we report the draft genome sequence of this strain together with features of the organism and generation, annotation and analysis of the genome sequence. The 11.5 Mb genome of Streptomyces hyaluromycini MB-PO13T encoded 10,098 putative ORFs, of which 5317 were assigned with COG categories. The genome harbored at least six type I PKS clusters, three type II PKS gene clusters, two type III PKS gene clusters, six NRPS gene clusters, and one hybrid PKS/NRPS gene cluster...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29340007/genomic-insights-into-mycobacterium-simiae-human-colonization
#13
José L Steffani-Vallejo, Marion E Brunck, Erika Y Acosta-Cruz, Rafael Montiel, Francisco Barona-Gómez
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...
2018: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29299111/genome-sequence-of-acuticoccus-yangtzensis-jl1095t-dsm-28604t-isolated-from-the-yangtze-estuary
#14
Lei Hou, Jia Sun, Xiabing Xie, Nianzhi Jiao, Yao Zhang
Acuticoccus yangtzensis JL1095T is a proteobacterium from a genus belonging to the family Rhodobacteraceae ; it was isolated from surface waters of the Yangtze Estuary, China. This strain displays the capability to utilize aromatic and simple carbon compounds. Here, we present the genome sequence, annotations, and features of A. yangtzensis JL1095T . This strain has a genome size of 5,043,263 bp with a G + C content of 68.63%. The genome contains 4286 protein-coding genes, 56 RNA genes, and 83 pseudo genes...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29299110/genome-of-russian-wheat-aphid-an-economically-important-cereal-aphid
#15
Nicolaas Francois Visser Burger, Anna-Maria Botha
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...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29299109/the-draft-genome-of-brucella-abortus-strain-ba-col-b012-isolated-from-a-dairy-farm-in-nari%C3%A3-o-colombia-bring-new-insights-into-the-epidemiology-of-biovar-4-strains
#16
Mauricio Pacheco-Montealegre, Rocío E Patiño, Ligia Torres, Sabrina Jiménez, José Luis Rodríguez, Alejandro Caro-Quintero
No abstract text is available yet for this article.
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29299108/complete-genome-sequence-of-esterase-producing-bacterium-croceicoccus-marinus-e4a9-t
#17
Yue-Hong Wu, Hong Cheng, Ying-Yi Huo, Lin Xu, Qian Liu, Chun-Sheng Wang, Xue-Wei Xu
Croceicoccus marinus E4A9T was 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)...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29276572/genome-sequence-of-the-model-plant-pathogen-pectobacterium-carotovorum-scc1
#18
Outi Niemi, Pia Laine, Patrik Koskinen, Miia Pasanen, Ville Pennanen, Heidi Harjunpää, Johanna Nykyri, Liisa Holm, Lars Paulin, Petri Auvinen, E Tapio Palva, Minna Pirhonen
Bacteria of the genus Pectobacterium are economically important plant pathogens that cause soft rot disease on a wide variety of plant species. Here, we report the genome sequence of Pectobacterium carotovorum strain SCC1, a Finnish soft rot model strain isolated from a diseased potato tuber in the early 1980's. The genome of strain SCC1 consists of one circular chromosome of 4,974,798 bp and one circular plasmid of 5524 bp. In total 4451 genes were predicted, of which 4349 are protein coding and 102 are RNA genes...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29276571/draft-genome-sequence-of-dethiosulfovibrio-salsuginis-dsm-21565-t-an-anaerobic-slightly-halophilic-bacterium-isolated-from-a-colombian-saline-spring
#19
Carolina Díaz-Cárdenas, Gina López, José David Alzate-Ocampo, Laura N González, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, Silvia Restrepo, Sandra Baena
A bacterium belonging to the phylum Synergistetes , genus Dethiosulfovibrio was isolated in 2007 from a saline spring in Colombia. Dethiosulfovibrio salsuginis USBA 82T ( DSM 21565 T = KCTC 5659 T ) 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 ...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/29276570/complete-genome-of-a-novel-virulent-phage-st0-lysing-escherichia-coli-h8
#20
Honghui Liu, Xinchun Liu, Jinqing Li
Phage ST0 lysing Escherichia coli H8 was isolated from wastewater and sequenced using an Illumina HiSeq system. Genomic analyses revealed that it was virulent phages and contained a circular double-stranded DNA genome, consisting of 170,496 nucleotides with an average G + C content of 37.67%. This study may provide possible alternative materials for phage therapy.
2017: Standards in Genomic Sciences
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