Thu, 21 Aug 2008 16:08:58 BST CiteULike: Author Dehal http://www.citeulike.org/author/Dehal CiteULike.org en-gb Copyright © 2004-2008 citeulike.org http://www.citeulike.org/user/neils/article/1090867 <i>Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588.</i><br /><br />We generated draft genome sequences for two cold-adapted Archaea, Methanogenium frigidum and Methanococcoides burtonii, to identify genotypic characteristics that distinguish them from Archaea with a higher optimal growth temperature (OGT). Comparative genomics revealed trends in amino acid and tRNA composition, and structural features of proteins. Proteins from the cold-adapted Archaea are characterized by a higher content of noncharged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15 degrees -98 degrees C) were used to generate 1111 modeled protein structures. Analysis of the models from the cold-adapted Archaea showed a strong tendency in the solvent-accessible area for more Gln, Thr, and hydrophobic residues and fewer charged residues. A cold shock domain (CSD) protein (CspA homolog) was identified in M. frigidum, two hypothetical proteins with CSD-folds in M. burtonii, and a unique winged helix DNA-binding domain protein in M. burtonii. This suggests that these types of nucleic acid binding proteins have a critical role in cold-adapted Archaea. Structural analysis of tRNA sequences from the Archaea indicated that GC content is the major factor influencing tRNA stability in hyperthermophiles, but not in the psychrophiles, mesophiles or moderate thermophiles. Below an OGT of 60 degrees C, the GC content in tRNA was largely unchanged, indicating that any requirement for flexibility of tRNA in psychrophiles is mediated by other means. This is the first time that comparisons have been performed with genome data from Archaea spanning the growth temperature extremes from psychrophiles to hyperthermophiles. Mechanisms of thermal adaptation revealed from the genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii. NF Saunders T Thomas PM Curmi JS Mattick E Kuczek R Slade J Davis PD Franzmann D Boone K Rusterholtz R Feldman C Gates S Bench K Sowers K Kadner A Aerts P Dehal C Detter T Glavina S Lucas P Richardson F Larimer L Hauser M Land R Cavicchioli doi:10.1101/gr.1180903 Genome Res, Vol. 13, No. 7. (July 2003), pp. 1580-1588. 2007-02-06T16:51:44-00:00 2003 Genome Res 1088-9051 13 7 1580 1588 antarctic bioinformatics genomics methanococcoides methanogenium psychrophily http://www.citeulike.org/group/5032/article/780209 <i>Science, Vol. 298, No. 5601. (13 December 2002), pp. 2157-2167.</i><br /><br />The first chordates appear in the fossil record at the time of the Cambrian explosion, nearly 550 million years ago. The modern ascidian tadpole represents a plausible approximation to these ancestral chordates. To illuminate the origins of chordate and vertebrates, we generated a draft of the protein-coding portion of the genome of the most studied ascidian, Ciona intestinalis. The Ciona genome contains approximately 16,000 protein-coding genes, similar to the number in other invertebrates, but only half that found in vertebrates. Vertebrate gene families are typically found in simplified form in Ciona, suggesting that ascidians contain the basic ancestral complement of genes involved in cell signaling and development. The ascidian genome has also acquired a number of lineage-specific innovations, including a group of genes engaged in cellulose metabolism that are related to those in bacteria and fungi. The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. P Dehal Y Satou RK Campbell J Chapman B Degnan A De Tomaso B Davidson A Di Gregorio M Gelpke DM Goodstein N Harafuji KE Hastings I Ho K Hotta W Huang T Kawashima P Lemaire D Martinez IA Meinertzhagen S Necula M Nonaka N Putnam S Rash H Saiga M Satake A Terry L Yamada HG Wang S Awazu K Azumi J Boore M Branno S Chin-Bow R DeSantis S Doyle P Francino DN Keys S Haga H Hayashi K Hino KS Imai K Inaba S Kano K Kobayashi M Kobayashi BI Lee KW Makabe C Manohar G Matassi M Medina Y Mochizuki S Mount T Morishita S Miura A Nakayama S Nishizaka H Nomoto F Ohta K Oishi I Rigoutsos M Sano A Sasaki Y Sasakura E Shoguchi T Shin-i A Spagnuolo D Stainier MM Suzuki O Tassy N Takatori M Tokuoka K Yagi F Yoshizaki S Wada C Zhang PD Hyatt F Larimer C Detter N Doggett T Glavina T Hawkins P Richardson S Lucas Y Kohara M Levine N Satoh DS Rokhsar doi:10.1126/science.1080049 Science, Vol. 298, No. 5601. (13 December 2002), pp. 2157-2167. 2006-07-30T10:15:17-00:00 2002 Science 1095-9203 298 5601 2157 2167 ci draft genome http://www.citeulike.org/user/wenhan/article/822669 <i>Science, Vol. 297, No. 5585. (23 August 2002), pp. 1301-1310.</i><br /><br />The compact genome of Fugu rubripes has been sequenced to over 95% coverage, and more than 80% of the assembly is in multigene-sized scaffolds. In this 365-megabase vertebrate genome, repetitive DNA accounts for less than one-sixth of the sequence, and gene loci occupy about one-third of the genome. As with the human genome, gene loci are not evenly distributed, but are clustered into sparse and dense regions. Some "giant" genes were observed that had average coding sequence sizes but were spread over genomic lengths significantly larger than those of their human orthologs. Although three-quarters of predicted human proteins have a strong match to Fugu, approximately a quarter of the human proteins had highly diverged from or had no pufferfish homologs, highlighting the extent of protein evolution in the 450 million years since teleosts and mammals diverged. Conserved linkages between Fugu and human genes indicate the preservation of chromosomal segments from the common vertebrate ancestor, but with considerable scrambling of gene order. Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. S Aparicio J Chapman E Stupka N Putnam JM Chia P Dehal A Christoffels S Rash S Hoon A Smit MD Gelpke J Roach T Oh IY Ho M Wong C Detter F Verhoef P Predki A Tay S Lucas P Richardson SF Smith MS Clark YJ Edwards N Doggett A Zharkikh SV Tavtigian D Pruss M Barnstead C Evans H Baden J Powell G Glusman L Rowen L Hood YH Tan G Elgar T Hawkins B Venkatesh D Rokhsar S Brenner doi:10.1126/science.1072104 Science, Vol. 297, No. 5585. (23 August 2002), pp. 1301-1310. 2006-08-31T03:01:32-00:00 2002 Science 1095-9203 297 5585 1301 1310 metagenomics_0208 http://www.citeulike.org/group/3842/article/1632464 <i>PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.</i><br /><br />Transcription factors (TFs) form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs), are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene–regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought. Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes Morgan Price Paramvir Dehal Adam Arkin doi:10.1371/journal.pcbi.0030175 PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175. 2007-09-07T19:49:10-00:00 2007 PLoS Computational Biology 3 9 e175 bacteria gene-regulation orthology transcription-factors http://www.citeulike.org/user/cjeans/article/1839772 <i>PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.</i><br /><br />Transcription factors (TFs) form large paralogous gene families and have complex evolutionary histories. Here, we ask whether putative orthologs of TFs, from bidirectional best BLAST hits (BBHs), are evolutionary orthologs with conserved functions. We show that BBHs of TFs from distantly related bacteria are usually not evolutionary orthologs. Furthermore, the false orthologs usually respond to different signals and regulate distinct pathways, while the few BBHs that are evolutionary orthologs do have conserved functions. To test the conservation of regulatory interactions, we analyze expression patterns. We find that regulatory relationships between TFs and their regulated genes are usually not conserved for BBHs in Escherichia coli K12 and Bacillus subtilis. Even in the much more closely related bacteria Vibrio cholerae and Shewanella oneidensis MR-1, predicting regulation from E. coli BBHs has high error rates. Using gene–regulon correlations, we identify genes whose expression pattern differs between E. coli and S. oneidensis. Using literature searches and sequence analysis, we show that these changes in expression patterns reflect changes in gene regulation, even for evolutionary orthologs. We conclude that the evolution of bacterial regulation should be analyzed with phylogenetic trees, rather than BBHs, and that bacterial regulatory networks evolve more rapidly than previously thought. Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes Morgan Price Paramvir Dehal Adam Arkin doi:10.1371/journal.pcbi.0030175#toclink5 PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175. 2007-10-30T09:58:25-00:00 2007 PLoS Computational Biology 3 9 e175 network regulation http://www.citeulike.org/user/stajich/article/1146925 <i>Nature Biotechnology, Vol. 25, No. 3. (04 March 2007), pp. 319-326.</i> Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis Thomas Jeffries Igor Grigoriev Jane Grimwood José Laplaza Andrea Aerts Asaf Salamov Jeremy Schmutz Erika Lindquist Paramvir Dehal Harris Shapiro Yong-Su Jin Volkmar Passoth Paul Richardson doi:10.1038/nbt1290 Nature Biotechnology, Vol. 25, No. 3. (04 March 2007), pp. 319-326. 2007-03-08T11:22:51-00:00 2007 Nature Biotechnology 1087-0156 25 3 319 326 Nature Publishing Group genome pichia http://www.citeulike.org/user/Iden-J_GluR/article/1053018 <i>Nature, Vol. 428, No. 6982. (1 April 2004), pp. 529-535.</i><br /><br />Chromosome 19 has the highest gene density of all human chromosomes, more than double the genome-wide average. The large clustered gene families, corresponding high G + C content, CpG islands and density of repetitive DNA indicate a chromosome rich in biological and evolutionary significance. Here we describe 55.8 million base pairs of highly accurate finished sequence representing 99.9% of the euchromatin portion of the chromosome. Manual curation of gene loci reveals 1,461 protein-coding genes and 321 pseudogenes. Among these are genes directly implicated in mendelian disorders, including familial hypercholesterolaemia and insulin-resistant diabetes. Nearly one-quarter of these genes belong to tandemly arranged families, encompassing more than 25% of the chromosome. Comparative analyses show a fascinating picture of conservation and divergence, revealing large blocks of gene orthology with rodents, scattered regions with more recent gene family expansions and deletions, and segments of coding and non-coding conservation with the distant fish species Takifugu. The DNA sequence and biology of human chromosome 19. J Grimwood LA Gordon A Olsen A Terry J Schmutz J Lamerdin U Hellsten D Goodstein O Couronne M Tran-Gyamfi A Aerts M Altherr L Ashworth E Bajorek S Black E Branscomb S Caenepeel A Carrano C Caoile YM Chan M Christensen CA Cleland A Copeland E Dalin P Dehal M Denys JC Detter J Escobar D Flowers D Fotopulos C Garcia AM Georgescu T Glavina M Gomez E Gonzales M Groza N Hammon T Hawkins L Haydu I Ho W Huang S Israni J Jett K Kadner H Kimball A Kobayashi V Larionov SH Leem F Lopez Y Lou S Lowry S Malfatti D Martinez P McCready C Medina J Morgan K Nelson M Nolan I Ovcharenko S Pitluck M Pollard AP Popkie P Predki G Quan L Ramirez S Rash J Retterer A Rodriguez S Rogers A Salamov A Salazar X She D Smith T Slezak V Solovyev N Thayer H Tice M Tsai A Ustaszewska N Vo M Wagner J Wheeler K Wu G Xie J Yang I Dubchak TS Furey P DeJong M Dickson D Gordon EE Eichler LA Pennacchio P Richardson L Stubbs DS Rokhsar RM Myers EM Rubin SM Lucas doi:10.1038/nature02399 Nature, Vol. 428, No. 6982. (1 April 2004), pp. 529-535. 2007-01-19T15:27:12-00:00 2004 Nature 1476-4687 428 6982 529 535 no-tag http://www.citeulike.org/user/jmeppley/article/825454 <i>Science, Vol. 313, No. 5791. (1 September 2006), pp. 1261-1266.</i><br /><br />Draft genome sequences have been determined for the soybean pathogen Phytophthora sojae and the sudden oak death pathogen Phytophthora ramorum. Oomycetes such as these Phytophthora species share the kingdom Stramenopila with photosynthetic algae such as diatoms, and the presence of many Phytophthora genes of probable phototroph origin supports a photosynthetic ancestry for the stramenopiles. Comparison of the two species' genomes reveals a rapid expansion and diversification of many protein families associated with plant infection such as hydrolases, ABC transporters, protein toxins, proteinase inhibitors, and, in particular, a superfamily of 700 proteins with similarity to known oomycete avirulence genes. 10.1126/science.1128796 Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis Brett Tyler Sucheta Tripathy Xuemin Zhang Paramvir Dehal Rays Jiang Andrea Aerts Felipe Arredondo Laura Baxter Douda Bensasson Jim Beynon Jarrod Chapman Cynthia Damasceno Anne Dorrance Daolong Dou Allan Dickerman Inna Dubchak Matteo Garbelotto Mark Gijzen Stuart Gordon Francine Govers Niklaus Grunwald Wayne Huang Kelly Ivors Richard Jones Sophien Kamoun Konstantinos Krampis Kurt Lamour Mi-Kyung Lee Hayes Mcdonald Monica Medina Harold Meijer Eric Nordberg Donald Maclean Manuel Ospina-Giraldo Paul Morris Vipaporn Phuntumart Nicholas Putnam Sam Rash Jocelyn Rose Yasuko Sakihama Asaf Salamov Alon Savidor Chantel Scheuring Brian Smith Bruno Sobral Astrid Terry Trudy Torto-Alalibo Joe Win Zhanyou Xu Hongbin Zhang Igor Grigoriev Daniel Rokhsar Jeffrey Boore doi:10.1126/science.1128796 Science, Vol. 313, No. 5791. (1 September 2006), pp. 1261-1266. 2006-09-01T18:39:26-00:00 2006 Science 313 5791 1261 1266 comparative-genomics http://www.citeulike.org/user/nickluscombe/article/804195 <i>Science, Vol. 293, No. 5527. (6 July 2001), pp. 104-111.</i><br /><br />To illuminate the function and evolutionary history of both genomes, we sequenced mouse DNA related to human chromosome 19. Comparative sequence alignments yielded confirmatory evidence for hypothetical genes and identified exons, regulatory elements, and candidate genes that were missed by other predictive methods. Chromosome-wide comparisons revealed a difference between single-copy HSA19 genes, which are overwhelmingly conserved in mouse, and genes residing in tandem familial clusters, which differ extensively in number, coding capacity, and organization between the two species. Finally, we sequenced breakpoints of all 15 evolutionary rearrangements, providing a view of the forces that drive chromosome evolution in mammals. Human chromosome 19 and related regions in mouse: conservative and lineage-specific evolution. P Dehal P Predki AS Olsen A Kobayashi P Folta S Lucas M Land A Terry CL Ecale Zhou S Rash Q Zhang L Gordon J Kim C Elkin MJ Pollard P Richardson D Rokhsar E Uberbacher T Hawkins E Branscomb L Stubbs doi:10.1126/science.1060310 Science, Vol. 293, No. 5527. (6 July 2001), pp. 104-111. 2006-08-17T13:49:36-00:00 2001 Science 0036-8075 293 5527 104 111 no-tag http://www.citeulike.org/user/xdeupi/article/375831 <i>PLoS Biol, Vol. 3, No. 10. (October 2005)</i><br /><br />The hypothesis that the relatively large and complex vertebrate genome was created by two ancient, whole genome duplications has been hotly debated, but remains unresolved. We reconstructed the evolutionary relationships of all gene families from the complete gene sets of a tunicate, fish, mouse, and human, and then determined when each gene duplicated relative to the evolutionary tree of the organisms. We confirmed the results of earlier studies that there remains little signal of these events in numbers of duplicated genes, gene tree topology, or the number of genes per multigene family. However, when we plotted the genomic map positions of only the subset of paralogous genes that were duplicated prior to the fish-tetrapod split, their global physical organization provides unmistakable evidence of two distinct genome duplication events early in vertebrate evolution indicated by clear patterns of four-way paralogous regions covering a large part of the human genome. Our results highlight the potential for these large-scale genomic events to have driven the evolutionary success of the vertebrate lineage. Two rounds of whole genome duplication in the ancestral vertebrate. P Dehal JL Boore doi:10.1371/journal.pbio.0030314 PLoS Biol, Vol. 3, No. 10. (October 2005) 2005-11-01T19:08:39-00:00 2005 PLoS Biol 1545-7885 3 10 genome