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Research: Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements
- Luis E. Valentin-Alvarado,
- Ling-Dong Shi,
- Kathryn E. Appler,
- Alexander Crits-Christoph,
- Valerie De Anda,
- Benjamin A. Adler,
- Michael L. Cui,
- Lynn Ly,
- Pedro Leão,
- Richard J. Roberts,
- Rohan Sachdeva,
- Brett J. Baker,
- David F. Savage,
- and Jillian F. Banfield
Genome Res. October 2024 34: 1595-1609; Published in Advance October 15, 2024, doi:10.1101/gr.279480.124
...Complete s of Asgard archaea reveal diverse integrated and mobile genetic elements Luis E. Valentin-Alvarado1,2, Ling-Dong Shi1, Kathryn E. Appler3, Alexander Crits-Christoph1,2,11, Valerie De Anda3,4, Benjamin A. Adler1, Michael L. Cui1, Lynn Ly5, Pedro Leão3,12, Richard J. Roberts6, Rohan...
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Research: Xylem systems genetics analysis reveals a key regulator of lignin biosynthesis in Populus deltoides
- Kelly M. Balmant,
- Jerald D. Noble,
- Filipe C. Alves,
- Christopher Dervinis,
- Daniel Conde,
- Henry W. Schmidt,
- Ana I. Vazquez,
- William B. Barbazuk,
- Gustavo de los Campos,
- Marcio F.R. Resende, Jr.,
- and Matias Kirst
Genome Res. August 2020 30: 1131-1143; Published in Advance August 19, 2020, doi:10.1101/gr.261438.120
...of biological information that underlies complex traits from genotype to phenotype. In this study, we used a systems genetics approach to identify and evaluate regulators of the lignin biosynthesis pathway in Populus deltoides by combining , transcriptome, and phenotype data from a population of 268 unrelated...
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LETTER: Conservation of the Biotin Regulon and the BirA Regulatory Signal in Eubacteria and Archaea
- Dmitry A. Rodionov,
- Andrei A. Mironov,
- and Mikhail S. Gelfand
Genome Res. October 1, 2002 12: 1507-1516; doi:10.1101/gr.314502
..., observed in several s, possibly represent the existence of different pathways for pimeloyl-CoA biosynthesis. Another interesting result of analysis of operon structures and BirA sites is that some biotin-dependent carboxylases from Rhodobacter capsulatus , actinomycetes, and archaea are possibly...
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LETTER: Genome Evolution at the Genus Level: Comparison of Three Complete Genomes of Hyperthermophilic Archaea
- Odile Lecompte,
- Raymond Ripp,
- Valérie Puzos-Barbe,
- Simone Duprat,
- Roland Heilig,
- Jacques Dietrich,
- Jean-Claude Thierry,
- and Olivier Poch
Genome Res. June 1, 2001 11: 981-993; Published in Advance May 8, 2001, doi:10.1101/gr.165301
...been lost in P. horikoshii since the divergence of P. abyssi and P. horikoshii (Fig. 1 C). We then looked for dispersed genetic elements that may promote the observed intergenomic disruption synteny. Putative targets for homologous recombination in Archaea are LCTRs detected previously in several...
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RESEARCH: Comparative Genomics of the Archaea (Euryarchaeota): Evolution of Conserved Protein Families, the Stable Core, and the Variable Shell
- Kira S. Makarova,
- L. Aravind,
- Michael Y. Galperin,
- Nick V. Grishin,
- Roman L. Tatusov,
- Yuri I. Wolf,
- and Eugene V. Koonin
Genome Res. July 1, 1999 9: 608-628; doi:10.1101/gr.9.7.608
...is likely (Table 1 ). The biosynthesis of branched chain aliphatic amino acids (leucine, isoleucine, valine) is an example of a complex pathway that is, in its entirety, represented by orthologs in the three autotrophic archaea as well as in most bacteria. This is, however, an exception rather than the rule...
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RESEARCH: Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily
- Christopher J. Leonard,
- L. Aravind,
- and Eugene V. Koonin
Genome Res. October 1, 1998 8: 1038-1047; doi:10.1101/gr.8.10.1038
...Novel Families of Putative Protein Kinases in Bacteria and Archaea: Evolution of the “Eukaryotic” Protein Kinase Superfamily Christopher J. Leonard 1 , L. Aravind 1 , 2 , and Eugene V. Koonin 1 , 3 1National Center for Biotechnology...
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Letter: Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis
- Boris U. Stambuk,
- Barbara Dunn,
- Sergio L. Alves, Jr,
- Eduarda H. Duval,
- and Gavin Sherlock
Genome Res. December 2009 19: 2271-2278; Published in Advance November 6, 2009, doi:10.1101/gr.094276.109
...Industrial fuel ethanol yeasts contain adaptive copy number changes in genes involved in vitamin B1 and B6 biosynthesis Boris U. Stambuk 1 , 2 , 3 , Barbara Dunn 1 , Sergio L. Alves, Jr 2 , Eduarda H. Duval 2 and Gavin Sherlock 1 , 3...
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ARTICLE: Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
- Neil F.W. Saunders,
- Torsten Thomas,
- Paul M.G. Curmi,
- John S. Mattick,
- Elizabeth Kuczek,
- Rob Slade,
- John Davis,
- Peter D. Franzmann,
- David Boone,
- Karl Rusterholtz,
- Robert Feldman,
- Chris Gates,
- Shellie Bench,
- Kevin Sowers,
- Kristen Kadner,
- Andrea Aerts,
- Paramvir Dehal,
- Chris Detter,
- Tijana Glavina,
- Susan Lucas,
- Paul Richardson,
- Frank Larimer,
- Loren Hauser,
- Miriam Land,
- and Ricardo Cavicchioli
Genome Res. July 2003 13: 1580-1588; Published in Advance June 12, 2003, doi:10.1101/gr.1180903
...Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii Neil F.W. Saunders 1 , Torsten Thomas 1 , 10 , Paul M.G. Curmi 2 , John S. Mattick 3 , Elizabeth Kuczek...
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RESEARCH: A Prokaryotic Gene Cluster Involved in Synthesis of Lysine through the Amino Adipate Pathway: A Key to the Evolution of Amino Acid Biosynthesis
- Hiromi Nishida,
- Makoto Nishiyama,
- Nobuyuki Kobashi,
- Takehide Kosuge,
- Takayuki Hoshino,
- and Hisakazu Yamane
Genome Res. December 1, 1999 9: 1175-1183; doi:10.1101/gr.9.12.1175
...of homoaconitase (HacA/Lys4A) of T. thermophilus is grouped with a protein, PH1726, of P. horikoshii (Fig. 3 B). This group is connected to the lineage of 3-isopropylmalate dehydratase (LeuC) homologs from A. aeolicus and three archaea, Archaeoglobus fulgidus ( Klenk et al. 1997 ), Methanobacterium...
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RESEARCH: Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence
- Hidemasa Bono,
- Hiroyuki Ogata,
- Susumu Goto,
- and Minoru Kanehisa
Genome Res. March 1, 1998 8: 203-210; doi:10.1101/gr.8.3.203
...Reconstruction of Amino Acid Biosynthesis Pathways from the Complete Genome Sequence Hidemasa Bono , Hiroyuki Ogata , Susumu Goto and Minoru Kanehisa 1 Institute for Chemical Research, Kyoto University, Uji, Kyoto 611, Japan...

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