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ARTICLE: Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes
- Toshiaki Fukui,
- Haruyuki Atomi,
- Tamotsu Kanai,
- Rie Matsumi,
- Shinsuke Fujiwara,
- and Tadayuki Imanaka
Genome Res. March 2005 15: 352-363; Published in Advance February 14, 2005, doi:10.1101/gr.3003105
...-reducing hyperthermophilic archaea, belongs to the order Thermococcales in Euryarchaeota along with the closely related genus Pyrococcus . The members of Thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity...
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Research: Parallel evolution of transcriptome architecture during genome reorganization
- Sung Ho Yoon,
- David J. Reiss,
- J. Christopher Bare,
- Dan Tenenbaum,
- Min Pan,
- Joseph Slagel,
- Robert L. Moritz,
- Sujung Lim,
- Murray Hackett,
- Angeli Lal Menon,
- Michael W.W. Adams,
- Adam Barnebey,
- Steven M. Yannone,
- John A. Leigh,
- and Nitin S. Baliga
Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
...challenges. However, the genome reorganization events that drive this process are also the roots of instability for existing operons. We have determined that there exists a statistically significant trend that correlates the proportion of genes encoded in operons in archaea to their phylogenetic lineage. We...
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Letter: Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations
- Ravi D. Barabote,
- Gary Xie,
- David H. Leu,
- Philippe Normand,
- Anamaria Necsulea,
- Vincent Daubin,
- Claudine Médigue,
- William S. Adney,
- Xin Clare Xu,
- Alla Lapidus,
- Rebecca E. Parales,
- Chris Detter,
- Petar Pujic,
- David Bruce,
- Celine Lavire,
- Jean F. Challacombe,
- Thomas S. Brettin,
- and Alison M. Berry
Genome Res. June 2009 19: 1033-1043; Published in Advance March 6, 2009, doi:10.1101/gr.084848.108
..._1626, Acel_1628, Acel_1634, Acel_1639, Acel_1643, and Acel_1644) encode proteins that bear highest sequence similarity to proteins from thermophilic bacteria and archaea. With the exception of Acel_1626, homologs of these six proteins do not occur in Frankia . In addition to the three major islands, 21...
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ARTICLE: Biosynthesis of Isoprenoids via Mevalonate in Archaea: The Lost Pathway
- Arian Smit and
- Arcady Mushegian
Genome Res. October 1, 2000 10: 1468-1484; doi:10.1101/gr.145600
...to result in a (random) loss of one of the two. Thus, once both paths are completed in a cell, one of them, i.e., the DXP path in the lineage leading to eukarya and archaea, or the mevalonate path in bacteria, is discarded. This and later events in the evolution of isoprenoid biosynthesis and lipid side...
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ARTICLE: Comparative Complete Genome Sequence Analysis of the Amino Acid Replacements Responsible for the Thermostability of Corynebacterium efficiens
- Yousuke Nishio,
- Yoji Nakamura,
- Yutaka Kawarabayasi,
- Yoshihiro Usuda,
- Eiichiro Kimura,
- Shinichi Sugimoto,
- Kazuhiko Matsui,
- Akihiko Yamagishi,
- Hisashi Kikuchi,
- Kazuho Ikeo,
- and Takashi Gojobori
Genome Res. July 2003 13: 1572-1579; doi:10.1101/gr.1285603
...with decreasing GC content reported in a statistical analysis of the complete s of six thermophilic archaea, two thermophilic bacteria, 17 mesophilic bacteria, and two eukaryotic species ( Kreil and Ouzounis 2001 ). On the other hand, the high frequency of Gly and Arg in C. efficiens concurs with the view...
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Research: A global network of coexisting microbes from environmental and whole-genome sequence data
- Samuel Chaffron,
- Hubert Rehrauer,
- Jakob Pernthaler,
- and Christian von Mering
Genome Res. July 2010 20: 947-959; Published in Advance May 10, 2010, doi:10.1101/gr.104521.109
...RNA covariance models of the RDP database (Cole et al. 2009). Before defining OTUs, we removed sequences for which the alignment had not been successful (i.e., Infernal bit-score < 0). OTUs were built for both Archaea and Bacteria by hierarchical clustering (complete linkage), at various distances (from 0.2 to 0...
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LETTER: Lineage-Specific Gene Expansions in Bacterial and Archaeal Genomes
- I. King Jordan,
- Kira S. Makarova,
- John L. Spouge,
- Yuri I. Wolf,
- and Eugene V. Koonin
Genome Res. April 1, 2001 11: 555-565; Published in Advance March 13, 2001, doi:10.1101/gr.166001
...duplication is an important mechanistic antecedent to the evolution of new genes and novel biochemical functions. In an attempt to assess the contribution of gene duplication to genome evolution in archaea and bacteria, clusters of related genes that appear to have expanded subsequent to the diversification...
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ARTICLE: Genome Sequence of an M3 Strain of Streptococcus pyogenes Reveals a Large-Scale Genomic Rearrangement in Invasive Strains and New Insights into Phage Evolution
- Ichiro Nakagawa,
- Ken Kurokawa,
- Atsushi Yamashita,
- Masanobu Nakata,
- Yusuke Tomiyasu,
- Nobuo Okahashi,
- Shigetada Kawabata,
- Kiyoshi Yamazaki,
- Tadayoshi Shiba,
- Teruo Yasunaga,
- Hideo Hayashi,
- Masahira Hattori,
- and Shigeyuki Hamada
Genome Res. June 2003 13: 1042-1055; doi:10.1101/gr.1096703
....T. 1999 . Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences. Genetics 152 : 1299 –1305. ↵ Makino, S. and Suzuki, M. 2001 . Bacterial genomic reorganization upon DNA replication. Science 292 : 803a . ↵ McShan, W.M., Tang, Y...
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ARTICLE: Genome sequence of Haloarcula marismortui: A halophilic archaeon from the Dead Sea
- Nitin S. Baliga,
- Richard Bonneau,
- Marc T. Facciotti,
- Min Pan,
- Gustavo Glusman,
- Eric W. Deutsch,
- Paul Shannon,
- Yulun Chiu,
- Rueyhung Sting Weng,
- Rueichi Richie Gan,
- Pingliang Hung,
- Shailesh V. Date,
- Edward Marcotte,
- Leroy Hood,
- and Wailap Victor Ng
Genome Res. November 2004 14: 2221-2234; doi:10.1101/gr.2700304
...architectures of Halobacterium sp . NRC-1 and H. marismortui suggests a common ancestor for the two organisms and a genome of significantly reduced size in the former. Both of these halophilic archaea use the same strategy of high surface negative charge of folded proteins as means to circumvent the salting...
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Resource: A single-base resolution map of an archaeal transcriptome
- Omri Wurtzel,
- Rajat Sapra,
- Feng Chen,
- Yiwen Zhu,
- Blake A. Simmons,
- and Rotem Sorek
Genome Res. January 2010 20: 133-141; Published in Advance November 2, 2009, doi:10.1101/gr.100396.109
...; 5 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA Abstract Organisms of the third domain of life, the Archaea, share molecular characteristics both with Bacteria and Eukarya. These organisms attract scientific attention as research models...

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