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Standards in Genomic Sciences

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
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
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
Yue-Hong Wu, Hong Cheng, Ying-Yi Huo, Lin Xu, Qian Liu, Chun-Sheng Wang, Xue-Wei Xu
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)...
2017: Standards in Genomic Sciences
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
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 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...
2017: Standards in Genomic Sciences
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
Raquel Quatrini, Lorena V Escudero, Ana Moya-Beltrán, Pedro A Galleguillos, Francisco Issotta, Mauricio Acosta, Juan Pablo Cárdenas, Harold Nuñez, Karina Salinas, David S Holmes, Cecilia Demergasso
10.1601/nm.2199 CLST is an extremely acidophilic gamma-proteobacteria that was isolated from the Gorbea salt flat, an acidic hypersaline environment in northern Chile. This kind of environment is considered a terrestrial analog of ancient Martian terrains and a source of new material for biotechnological applications. 10.1601/nm.2199 plays a key role in industrial bioleaching; it has the capacity of generating and maintaining acidic conditions by producing sulfuric acid and it can also remove sulfur layers from the surface of minerals, which are detrimental for their dissolution...
2017: Standards in Genomic Sciences
Ananda Shankar Bhattacharjee, Amir Mohaghegh Motlagh, Eddie B Gilcrease, Md Imdadul Islam, Sherwood R Casjens, Ramesh Goel
A lytic bacteriophage RG-2014 infecting a biofilm forming multidrug resistant bacterium Delftia tsuruhatensis strain ARB-1 as its host was isolated from a full-scale municipal wastewater treatment plant. Lytic phage RG-2014 was isolated for developing phage based therapeutic approaches against Delftia tsuruhatensis strain ARB-1. The strain ARB-1 belongs to the Comamonadaceae family of the Betaproteobacteria class. RG-2014 was characterized for its type, burst size, latent and eclipse time periods of 150 ± 9 PFU/cell, 10-min, <5-min, respectively...
2017: Standards in Genomic Sciences
Akbar Adjie Pratama, Irshad Ul Haq, Rashid Nazir, Maryam Chaib De Mares, Jan Dirk van Elsas
Here, we report the draft genome sequences of three fungal-interactive 10.1601/nm.27008 strains, denoted BS110, BS007 and BS437. Phylogenetic analyses showed that the three strains belong to clade II of the genus 10.1601/nm.1619, which was recently renamed 10.1601/nm.26956. This novel genus primarily contains environmental species, encompassing non-pathogenic plant- as well as fungal-interactive species. The genome of strain BS007 consists of 11,025,273 bp, whereas those of strains BS110 and BS437 have 11,178,081 and 11,303,071 bp, respectively...
2017: Standards in Genomic Sciences
Nils-Kåre Birkeland, Peter Schönheit, Lianna Poghosyan, Anne Fiebig, Hans-Peter Klenk
Archaeoglobus fulgidus is the type species of genus Archaeoglobus Stetter 1998, a hyperthermophilic sulfate reducing group within the Archaeoglobi class of the euryarchaeota phylum. Members of this genus grow heterotrophically or chemolithoautotrophically with sulfate or thiosulfate as electron acceptors. Except for A. fulgidus strain 7324 and the candidate species "Archaeoglobus lithotrophicus", which both originate from deep oil-fields, the other members of this genus have been recovered from marine hydrothermal systems...
2017: Standards in Genomic Sciences
Fernando Uriel Rojas-Rojas, Erika Yanet Tapia-García, Maskit Maymon, Ethan Humm, Marcel Huntemann, Alicia Clum, Manoj Pillay, Krishnaveni Palaniappan, Neha Varghese, Natalia Mikhailova, Dimitrios Stamatis, T B K Reddy, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Tanja Woyke, Nicole Shapiro, Ann M Hirsch, Paulina Estrada-de Los Santos
10.1601/nm.26956 caballeronis is a plant-associated bacterium. Strain TNe-841T was isolated from the rhizosphere of tomato (Solanum lycopersicum L. var. lycopersicum) growing in Nepantla Mexico State. Initially this bacterium was found to effectively nodulate Phaseolus vulgaris L. However, from an analysis of the genome of strain TNe-841T and from repeat inoculation experiments, we found that this strain did not nodulate bean and also lacked nodulation genes, suggesting that the genes were lost. The genome consists of 7,115,141 bp with a G + C content of 67...
2017: Standards in Genomic Sciences
Gina López, Carolina Diaz-Cárdenas, Nicole Shapiro, Tanja Woyke, Nikos C Kyrpides, J David Alzate, Laura N González, Silvia Restrepo, Sandra Baena
Here we present the physiological features of Pseudomonas extremaustralis strain USBA-GBX-515 (CMPUJU 515), isolated from soils in Superparamo ecosystems, > 4000 m.a.s.l, in the northern Andes of South America, as well as the thorough analysis of the draft genome. Strain USBA-GBX-515 is a Gram-negative rod shaped bacterium of 1.0-3.0 μm × 0.5-1 μm, motile and unable to form spores, it grows aerobically and cells show one single flagellum. Several genetic indices, the phylogenetic analysis of the 16S rRNA gene sequence and the phenotypic characterization confirmed that USBA-GBX-515 is a member of Pseudomonas genus and, the similarity of the 16S rDNA sequence was 100% with P...
2017: Standards in Genomic Sciences
Matías Castro, Ana Moya-Beltrán, Paulo C Covarrubias, Mónica Gonzalez, Juan Pablo Cardenas, Francisco Issotta, Harold Nuñez, Lillian G Acuña, Gonzalo Encina, David S Holmes, D Barrie Johnson, Raquel Quatrini
Acidithiobacillus albertensis is an extremely acidophilic, mesophilic, obligatory autotrophic sulfur-oxidizer, with potential importance in the bioleaching of sulfidic metal ores, first described in the 1980s. Here we present the draft genome sequence of Acidithiobacillus albertensis DSM 14366T, thereby both filling a long-standing gap in the genomics of the acidithiobacilli, and providing further insight into the understanding of the biology of the non iron-oxidizing members of the Acidithiobacillus genus...
2017: Standards in Genomic Sciences
Miho Watanabe, Riho Tokizawa, Hisaya Kojima, Manabu Fukui
10.1601/nm.25721 strain skLN1T is the type strain of the type species in the genus 10.1601/nm.25720 which is the one of the genera in the family 10.1601/nm.5070 within the phylum 10.1601/nm.3874. 10.1601/nm.25721 strain skLN1T is a Gram-positive, spore-forming thermophilic neutrophile isolated from freshwater lake sediment. Here, we present the draft genome sequence of strain skLN1T, which consists of 3,902,380 bp with a G + C content of 50.38%.
2017: Standards in Genomic Sciences
Marianna Nagymihály, Bálint M Vásarhelyi, Quentin Barrière, Teik-Min Chong, Balázs Bálint, Péter Bihari, Kar-Wai Hong, Balázs Horváth, Jamal Ibijbijen, Mohammed Amar, Attila Farkas, Éva Kondorosi, Kok-Gan Chan, Véronique Gruber, Pascal Ratet, Peter Mergaert, Attila Kereszt
Strain CCMM B554, also known as FSM-MA, is a soil dwelling and nodule forming, nitrogen-fixing bacterium isolated from the nodules of the legume Medicago arborea L. in the Maamora Forest, Morocco. The strain forms effective nitrogen fixing nodules on species of the Medicago, Melilotus and Trigonella genera and is exceptional because it is a highly effective symbiotic partner of the two most widely used accessions, A17 and R108, of the model legume Medicago truncatula Gaertn. Based on 16S rRNA gene sequence, multilocus sequence and average nucleotide identity analyses, FSM-MA is identified as a new Ensifer meliloti strain...
2017: Standards in Genomic Sciences
Aregu Amsalu Aserse, Tanja Woyke, Nikos C Kyrpides, William B Whitman, Kristina Lindström
The type strain of the prospective 10.1601/nm.30737 sp. nov. ERR11T, was isolated from a nodule of the leguminous tree Erythrina brucei native to Ethiopia. The type strain 10.1601/nm.1463 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T, was isolated from the nodules of Lespedeza cuneata in Beijing, China. The genomes of ERR11T and 10.1601/strainfinder?urlappend=%3Fid%3DCCBAU+10071 T were sequenced by DOE-JGI and deposited at the DOE-JGI genome portal as well as at the European Nucleotide Archive. The genome of ERR11T is 9,163,226 bp in length and has 102 scaffolds, containing 8548 protein-coding and 86 RNA genes...
2017: Standards in Genomic Sciences
Inés Martínez-Raudales, Yumiko De La Cruz-Rodríguez, Alejandro Alvarado-Gutiérrez, Julio Vega-Arreguín, Ahuitz Fraire-Mayorga, Miguel Alvarado-Rodríguez, Victor Balderas-Hernández, Saúl Fraire-Velázquez
A Bacillus velezensis strain from the rhizosphere of Sporobolus airoides (Torr.) Torr., a grass in central-north México, was isolated during a biocontrol of phytopathogens scrutiny study. The 2A-2B strain exhibited at least 60% of growth inhibition of virulent isolates of phytopathogens causing root rot. These phytopathogens include Phytophthora capsici, Fusarium solani, Fusarium oxysporum and Rhizoctonia solani. Furthermore, the 2A-2B strain is an indolacetic acid producer, and a plant inducer of PR1, which is an induced systemic resistance related gene in chili pepper plantlets...
2017: Standards in Genomic Sciences
Nikola Palevich, William J Kelly, Sinead C Leahy, Eric Altermann, Jasna Rakonjac, Graeme T Attwood
Butyrivibrio hungatei MB2003 was isolated from the plant-adherent fraction of rumen contents from a pasture-grazed New Zealand dairy cow, and was selected for genome sequencing in order to examine its ability to degrade plant polysaccharides. The genome of MB2003 is 3.39 Mb and consists of four replicons; a chromosome, a secondary chromosome or chromid, a megaplasmid and a small plasmid. The genome has an average G + C content of 39.7%, and encodes 2983 putative protein-coding genes. MB2003 is able to use a variety of monosaccharide substrates for growth, with acetate, butyrate and formate as the principal fermentation end-products, and the genes encoding these metabolic pathways have been identified...
2017: Standards in Genomic Sciences
Laura T Morales, Laura N González-García, María C Orozco, Silvia Restrepo, Martha J Vives
Crude oil contamination of soils and waters is a worldwide problem, which has been actively addressed in recent years. Sequencing genomes of microorganisms involved in the degradation of hydrocarbons have allowed the identification of several promoters, genes, and degradation pathways of these contaminants. This knowledge allows a better understanding of the functional dynamics of microbial degradation. Here, we report a first draft of the 44.2 Mbp genome assembly of an environmental strain of the fungus Scedosporium apiospermum...
2017: Standards in Genomic Sciences
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