Standards in Genomic Sciences


Vol 9, No 3 (2013): Standards in Genomic Sciences

Table of Contents

Genome Report

Complete genome sequence of Granulicella tundricola type strain MP5ACTX9T, an Acidobacteria from tundra soil
Suman R. Rawat, Minna K Männistö, Valentin Starovoytov, Lynne Goodwin, Matt Nolan, Loren J. Hauser, Miriam Land, Karen Walston Davenport, Tanja Woyke, Max M Häggblom
Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T).
Kemanthi Nanadasena, Ron Yates, Ravi Tiwari, Graham O'Hara, John Howieson, Mohamed Ninawi, Olga Chertkov, Chris Detter, Roxanne Tapia, Shunseng Han, Tanja Woyke, Sam Pitluck, Matt Nolan, Miriam Land, Konstantinos Liolios, Amrita Pati, Alex Copeland, Nikos C. Kyrpides, Natalia Ivanova, Lynne Goodwin, Uma Meenakshi, Wayne Reeve
Genome sequence of Ensifer arboris strain LMG 14919T; a microsymbiont of the legume Prosopis chilensis growing in Kosti, Sudan.
Wayne Gerald Reeve, Rui Tian, Lambert Brau, Lynne Goodwin, Christine Munk, Chris Detter, Roxanne Tapia, Cliff Han, Konstantinos Liolios, Marcel Huntemann, Amrita Pati, Tanja Woyke, Konstantinos Mavrommatis, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Anne Willems
Genome sequence of Burkholderia mimosarum strain LMG 23256T; a Mimosa pigra microsymbiont from Anso, Taiwan.
Anne Willems, Rui Tian, Lambert Brau, Lynne Goodwin, James Han, Konstantinos Liolios, Marcel Huntemann, Amrita Pati, Tanja Woyke, Konstantinos Mavrommatis, Victor Markowitz, Natalia Ivanova, Nikos Kyrpides, Wayne Gerald Reeve
Genome sequence of the chromate-resistant bacterium Leucobacter salsicius type strain M1-8T
Ji-Hyun Yun, Yong-Joon Cho, Jong-Sik Chun, Dong-Wook Hyun, Jin-Woo Bae
Genome sequence of the squalene-degrading bacterium Corynebacterium terpenotabidum type strain Y-11T (= DSM 44721T)
Christian Rückert, Andreas Albersmeier, Arwa Al-Dilaimi, Hanna Bednarz, Karsten Niehaus, Rafael Szczenpanowski, Jörn Kalinowski
Genome sequence of Ensifer medicae strain WSM1115; an acid-tolerant Medicago-nodulating microsymbiont from Samothraki, Greece.
Wayne Gerald Reeve, Ross Ballard, John Howieson, Elizabeth Drew, Rui Tian, Lambert Bräu, Christine Munk, Karen Davenport, Patrick Chain, Lynne Goodwin, Ioanna Pagani, Marcel Huntemann, Konstantinos Mavromatis, Amrita Pati, Victor Markowitz, Natalia Ivanoca, Tanja Woyke, Nikos Kyrpides
Genome sequence of Rhizobium leguminosarum bv trifolii strain WSM1689, the microsymbiont of the one flowered clover Trifolium uniflorum.
Jason Terpolilli, Rui Tian, Ron Yates, John Howieson, Philip Poole, Christine Munk, Roxanne Tapia, Cliff Han, Victor Markowitz, Reddy Tatiparthi, Konstantinos Mavromatis, Natalia Ivanova, Amrita Pati, Lynne Goodwin, Nikos Kyrpides, Nikos Kyrpides, Wayne Reeve
Genome sequence of the Listia angolensis microsymbiont Microvirga lotononidis strain WSM3557T
Wayne Gerald Reeve, Julie Ardley, Rui Tian, Sofie De Meyer, Jason Terpolilli, Vanessa Melino, Ravi Tiwari, Ronald Yates, Graham O'Hara, John Howieson, Mohamed Ninawi, Xiaojing Zhang, David Bruce, Chris Detter, Roxanne Tapia, Cliff Han, Chia-Lin Wei, Marcel Huntemann, James Han, I-Min Chen, Konstantinos Mavromatis, Victor Markowitz, Ernest Szeto, Natalia Ivanova, Ioanna Pagani, Amrita Pati, Lynne Goodwin, Tanja Woyke, Nikos C. Kyrpides
Genome sequence of the acid-tolerant Burkholderia sp. strain WSM2230 from Karijini National Park, Australia
Wayne Gerald Reeve, Elizabeth Watkin, Rui Tian, Lambert Bräu, Graham O'Hara, Lynne Goodwin, James Han, Elizabeth Lobos, Marcel Huntemann, Amrita Pati, Tanja Woyke, Konstantinos Mavormatis, Victor Markowitz, Natalia Ivanova, Nikos C. Kyrpides, Wayne Reeve
Complete genome sequence of Anabaena variabilis ATCC 29413
Teresa Thiel, Brenda S. Pratte, Jinshun Zhong, Lynne Goodwin, Alex Copeland, Susan Lucas, Cliff Han, Sam Pitluck, Miriam L. Land, Nikos C. Kyrpides, Tanja Woyke
Genomic analysis of Agrobacterium radiobacter DSM 30147T and emended description of A. radiobacter (Beijerinck and van Delden 1902) Conn 1942 (Approved Lists 1980) emend. Sawada et al. 1993
Linshuang Zhang, Xiangyang Li, Feng Zhang, Geijao Wang
Genome sequence of the Medicago-nodulating Ensifer meliloti commercial inoculant strain RRI128
Wayne Gerald Reeve, Ross Ballard, Elizabeth Drew, Rui Tian, Lambert Bräu, Lynne Goodwin, Marcel Huntemann, James Han, Reddy Tatiparthi, Amy Chen, Konstantinos Mavromatis, Victor Markowitz, Krishna Palaniappan, Natalia Ivanova, Amrita Pati, Tanja Woyke, Nikos Kyrpides
Draft genome sequence of Gluconobacter thailandicus NBRC 3257
Minenosuke Matsutani, Haruo Suzuki, Toshiharu Yakushi, Kazunobu Matsushita
High-quality draft genome sequence of nematocidal Bacillus thuringiensis Sbt003
Yingying Liu, Weixing Ye, Jinshui Zheng, Lei Fang, Donghai Peng, Lifang Ruan, Ming Sun
Draft genome sequence of marine alphaproteobacterial strain HIMB11, the first cultivated representative of a unique lineage within the Roseobacter clade possessing an unusually small genome
Bryndan Durham, Jana Grote, Kerry Whittaker, Sara Bender, Haiwei Luo, Sharon Grim, Julia Brown, John Casey, Antony Dron, Lennis Florez-Leiva, Andreas Krupke, Catherine Luria, Aric Mine, Olivia Nigro, Santhiska Pather, Agathe Talarmin, Emma Wear, Thomas Weber, Jesse Wilson, Matthew Church, Edward DeLong, David Karl, Grieg Steward, John Eppley, Nikos Kyrpides, Stephan Schuster, Michael Rappe
Genome sequence of the facultative anaerobic bacterium Bacillus sp. strain ZYK, a selenite and nitrate reducer from paddy soil
Peng Bao, Jian-Qiang Su, Zheng-Yi Hu, Max M. Häggblom, Yong-Guan Zhu
Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum carboxydivorans as a later syrnonym of D. nigrificans.
Michael Visser, Sofiya N. Parshina, Joana I. Alves, Diana Z. Sousa, Inês A. C. Pereira, Gerard Muyzer, Jan Kuever, Alexander V. Lebedinsky, Jasper J. Koehorst, Petra Worm, Caroline M. Plugge, Peter J. Schaap, Lynne A. Goodwin, Alla Lapidus, Nikos C. Kyrpides, Tanja Woyke, Patrick Chain, Karen W. Davenport, Stefan Spring, Manfred Rohde, Hans-Peter Klenk, Alfons J.M. Stams
High quality draft genome sequence of Streptomyces sp. strain AW19M42 isolated from a sea squirt in Northern Norway
Gro Elin Kjæreng Bjerga, Erik Hjerde, Concetta De Santi, Adele Kim Williamson, Arne Oskar Smalås, Nils Peder Willassen, Bjørn Altermark
Genome sequence of Leisingera nanhaiensis strain DSM 24252T isolated from marine sediment
Sven Breider, Hazuki Teshima, Jörn Petersen, Olga Chertkov, Hajnalka Dalingault, Amy Chen, Amrita Pati, Natalia Ivanova, Alla Lapidus, Lynne A. Goodwin, Patrick Chain, John C. Detter, Manfred Rohde, Brian J. Tindall, Nikos C. Kyrpides, Tanja Woyke, Meinhard Simon, Markus Göker, Hans-Peter Klenk, Thorsten Brinkhoff
Non-contiguous finished genome sequence and description of Fenollaria massiliensis gen. nov., sp. nov., a new genus of anaerobic bacterium
Isabelle Pagnier, Olivier Croce, Catherine Robert, Didier Raoult, Bernard La Scola
Complete genome sequence of a plant associated bacterium Bacillus amyloliquefaciens strain UCMB5033
Adnan Niazi, Shahid Manzoor, Sarosh Bejai, Johan Meijer, Erik Bongcam-Rudloff
Complete genome of the switchgrass endophyte Enterobacter clocace P101
Jodi L. Humann, Mark Wildung, Derek Pouchnik, Austin A. Bates, Jennifer C. Drew, Ursula N. Zipperer, Eric W. Triplett, Dorrie Main, Brenda K. Schroeder
Non-contiguous finished genome sequence of Anoxybacillus flavithermus subsp. yunnanensis type strain (E13T), a strictly thermophilic and organic solvent-tolerant bacterium
Ying Wang, Yunyun Zheng, Min Wang, Yi Gao, Yazhong Xiao, Peng Hui
Genome sequence of the exopolysaccharide-producing Salipiger mucosus type strain (A3T), a moderately halophilic member of the Roseobacter clade
Markus Göker, Thomas Riedel, Stefan Spring, Anne Fiebig, Jörn Petersen, Nikos C. Kyrpides, Hans-Peter Klenk
Draft genome sequences and description of Lactobacillus rhamnosus strains LR-L31, LR-L34, and LR-L35
Prapaporn Boonma, Jennifer K. Spinler, Xiang Qin, Chutima Jittaprasatsin, Donna M. Muzny, Harsha Doddapaneni, Richard Gibbs, Joe Petrosino, Somying Tumwarsorn, James Versalovic
High quality draft genome sequence of Staphylococcus cohnii subsp. cohnii strain hu-01
xinjun hu, ang li, longxian lv, chunhui yuan, lihua guo, xiawei jiang, haiyin jiang, guirong qian, beiwen zheng, jing guo, lanjuan li
Non-contiguous finished genome sequence and description of Alistipes massilioanorexius sp. nov.
Anne Pfeiderer, Ajay kumar Mishra, Jean-Christophe lagier, Catherine Robert, Aurelia Caputo, Didier Raoult, Pierre-Edouard Fournier
Complete Genome sequence of Burkholderia phymatum STM815, a broad host range and efficient nitrogen-fixing symbiont of Mimosa species
Lionel Moulin
Draft genome sequence of Bacillus amyloliquefaciens HB-26
Xiao-yan Liu, Yong Min, Kai-Mei Wang, Zhong-Yi Wan, Zhi-Gang Zhang, Chun-Xia Cao, Rong-Hua Zhou, Ai-Bing Jiang, Cui-Jun Liu, Guang-Yang Zhang, Xian-Liang Cheng, Wei Zhang, Zi-Wen Yang
High quality draft genome sequence of Olivibacter sitiensis type strain (AW-6T), a diphenol degrader with genes involved in the catechol pathway
GEBA GEBA
Non-contiguous finished genome sequence and description of Bacteroides neonati sp. nov., a new species of anaerobic bacterium
Bernard La Scola
Non contiguous-finished genome sequence and description of Gorillabacterium massiliensis gen. nov, sp. nov., a new member of the Family Paenibacillaceae
Mamadou Bhoye Keita, Roshan Padhmanabhan, Aurelia Caputo, Catherine Robert, Eric Delaporte, Didier Raoult, Pierre-Edouard Fournier, Fadi Bittar
Genome analysis of Desulfotomaculum gibsoniae strain GrollT a highly versatile Gram-positive sulfate-reducing bacterium
Jan Kuever, Michael Visser, Claudia Loeffler, Matthias Boll, Petra Worm, Dina Z. Sousa, Caroline M. Plugge, Peter J. Schaap, Gerard Muyzer, Ines A.C. Pereira, Sofiya N. Pashina, Lynne A Goodwin, Nikos C. Kyrpides, Janine Detter, Tanja Woyke, Patrick Chain, Karen W. Davenport, Manfred Rohde, Stefan Spring, Hans-Peter KLenk, Alfons J.M. Stams
Complete genome sequence of the bacteriochlorophyll a-containing Roseibacterium elongatum type strain (DSM 19469T), a representative of the Roseobacter clade isolated from Australian coast sand
Thomas Riedel, Anne Fiebig, Markus Göker, Hans-Peter Klenk
Genome sequence of the Wenxinia marina type strain (DSM 24838T), a representative of the Roseobacter clade isolated from oilfield sediments
Thomas Riedel, Anne Fiebig, James Han, Marcel Huntemann, Stefan Spring, Jörn Petersen, Natalia N. Ivanova, Victor Markowitz, Tanja Woyke, Markus Göker, Nikos C. Kyrpides, Hans-Peter Klenk
Genome sequence and description of Neterenkonia massiliensis sp. nov.
Sophie Edouard, Senthil Sankar, Nicole Prisca Makaya Dangui, Jean-Christophe Lagier, Caroline Michelle, Didier Raoult, Pierre-Edouard Fournier
Draft genome sequence of Dyadobacter tibetensis type strain (Y620-1) isolated from glacial ice
Liu Yongqin, Anyi Hu, Liang Shen, Tandong Yao, Nianzhi Jiao, Ninglian Wang, Baiqin Xu
Complete genome sequence of Thalassolituus oleivorans R6-15, an obligate hydrocarbonoclastic marine bacterium from the Arctic Ocean
Chunming Dong, Xin Chen, Yanrong Xie, Qiliang Lai, Zongze Shao
Genome sequence of the pink to light reddish-pigmented Rubellimicrobium mesophilum type strain (DSM 19309T), a representative of the Roseobacter clade isolated from soil, and emended description of the species
Markus Göker, Anne Fiebig, Hans-Peter Klenk, Jörn Petersen, Stefan Spring, Thomas Riedel
Complete genome sequence of the Phaeobacter gallaeciensis type strain CIP 105210T (= DSM 26640T = BS107T)
Oliver Frank, Silke Pradella, Manfred Rohde, Carmen Scheuner, Hans-Peter Klenk, Markus Göker, Joern Petersen
The Genome Sequence of a Type ST239 Methicillin-Resistant Staphylococcus aureus Isolate from a Malaysian Hospital
Lian Shien Lee, Lay Kek Teh, Zainul Fadziruddin Zainuddin, Mohd. Zaki Salleh
Complete genome sequence of invertebrate iridovirus IIV22A, a variant of IIV22, isolated originally from a blackfly larva
Benoît Piégu, Sébastien Guizard, Tan Yeping, Corrine Cruaud, Arnault Couloux, Dennis K Bideshi, Brian A Federici, Yves Bigot
Non-contiguous finished genome sequence of Corynebacterium timonense type strain 5401744T
Veronique Roux, Catherine Robert, Didier Raoult

Community Dialog

Meeting Report: GBIF hackathon-workshop on Darwin Core and sample data (22-24 May 2013)
John Wieczorek, Olaf Banki, Stan Blum, John Deck, Markus Döring, Gabriele Dröge, Dag Endresen, Philip Goldstein, Patrick Leary, Leonard Krishtalka, Eamonn O'Tuama, Robert J Robbins, Tim Robertson, Pelin Yilmaz
Report of the 14th Genomic Standards Consortium Meeting, Oxford, UK, September 17-21, 2012
Neil Davies, Dawn Field, Linda Amaral-Zettler, Mesude Bicak, Sarah Bourlat, Jonathan Coddington, John Deck, Alexei Drummond, Jack A Gilbert, Frank Oliver Glöckner, Renzo Kottmann, Chris Meyer, Norman Morrison, Matthias Obst, Robert Robbins, Lynn Schriml, Peter Sterk, Steven Stones-Havas
Meeting report: Ocean ‘omics science, technology and cyberinfrastructure : current challenges and future requirements (August 20-23, 2013)
Jack A Gilbert, Gregory Dick, Bethany Jenkins, John Heidelberg, Eric Allen, Katherine Mackey, Edward DeLong

White Paper

Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project
Nikos C. Kyrpides, Tanja Woyke, Jonathan A. Eisen, George Garrity, Timothy G. Lilburn, Brian J. Beck, William B. Whitman, Phil Hugenholtz, Hans-Peter Klenk

Research Article

Metagenomic analysis of microbial consortium from natural crude oil that seeps into the marine ecosystem offshore Southern California
Erik R. Hawley, Hailan Piao, Nicole M. Scott, Stephanie Malfatti, Ioanna Pagani, Marcel Huntemann, Amy Chen, Tijana Glavina del Rio, Brian Foster, Alex Copeland, Janet Jansson, Amrita Pati, Jack A Gilbert, Susannah Tringe, Thomas D Lorenson, Matthias Hess

Editorial/Commentary

Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records
Scott Federhen, Karen Clark, Tanya Barrett, James Ostell, Helen Parkinson, Yuichi Kodama, Jun Mashima, Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi
Genomic Standards Consortium Projects
Dawn Field, Peter Sterk, Renzo Kottmann, Wim De Smet, Linda Amaral-Zettler, Guy Cochrane, Cole R James, Neil Davies, Peter Dawyndt, George M Garrity, Jack A Gilbert, Frank Oliver Glöckner, Lynette Hirschman, Hans-Peter Klenk, Rob Knight, Nikos Kyrpides, Folker Meyer, Ilene Karsch-Mizrachi, Norman Morrison, Robert Robbins, Inigo San Gil, Susanna Sansone, Lynn Schriml, Tatiana Tatusova, Dave Ussery, Pelin Yilmaz, Owen White, John Wooley, Gregory Caporaso
Meeting report from the fourth meeting of the Computational Modeling in Biology Network (COMBINE)
Dagmar Waltemath, Frank T Bergmann, Claudine Chaouiya, Tobias Czauderna, Padraig Gleeson, Carole Goble, Martin Golebiewski, Mickael Hucka, Nick Juty, Olga Krebs, Nicolas Le Novère, Huaiyu Mi, Ion I Moraru, Chris J Myers, David Nickerson, Brett G Olivier, Nicolas Rodriguez, Falk Schreiber, Lucian Smith, Fengkai Zhang, Eric Bonnet


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Acknowledgements

We would like to gratefully acknowledge the support of many members of the Genomic Standards Consortium, the broader genomic science community, and those who have indicated their willingness to serve as editors, reviewers and contributors.

SIGS was founded with grants from the Office of the Vice President for Research and Graduate Studies at Michigan State University, the Michigan State University Foundation, and the US Department of Energy Biological and Environmental Research DE-FG02-08ER64707. The journal became self-supporting on October 1, 2011.

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