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1. Complete genome sequence of Thermobispora bispora type strain (R51).

Author

Liolios, Konstantinos, Sikorski, Johannes, Jando, Marlen, Lapidus, Alla, Copeland, Alex, Glavina, Tijana, Del Rio, Nolan, Matt, Lucas, Susan, Tice, Hope, Cheng, Jan-Fang, Han, Cliff, Woyke, Tanja, Goodwin, Lynne, Pitluck, Sam, Ivanova, Natalia, Mavromatis, Konstantinos, Mikhailova, Natalia, Chertkov, Olga, Kuske, Cheryl, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Detter, John C, Brettin, Thomas, Rohde, Manfred, Göker, Markus, Bristow, James, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Klenk, Hans-Peter, and Kyrpides, Nikos C

Subjects
GEBA, Streptosporangineae, Two distinct 16S rRNA genes, non-pathogenic, strictly thermophilic, Biotechnology, Genetics, Human Genome, Biochemistry and Cell Biology
Abstract

Thermobispora bispora (Henssen 1957) Wang et al. 1996 is the type species of the genus Thermobispora. This genus is of great interest because it is strictly thermophilic and because it has been shown for several of its members that the genome contains substantially distinct (6.4% sequence difference) and transcriptionally active 16S rRNA genes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member from the suborder Streptosporangineae and the first genome sequence of a member of the genus Thermobispora. The 4,189,976 bp long genome with its 3,596 protein-coding and 63 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

Published
2010

2. The Genome of the Diatom Thalassiosira pseudonana: Ecology, Evolution, and Metabolism

Author

Armbrust, E. Virginia, Berges, John A., Bowler, Chris, Green, Beverley R., Martinez, Diego, Putnam, Nicholas H., Zhou, Shiguo, Allen, Andrew E., Apt, Kirk E., Bechner, Michael, Brzezinski, Mark A., Chaal, Balbir K., Chiovitti, Anthony, Davis, Aubrey K., Demarest, Mark S., Detter, J. Chris, Glavina, Tijana, Goodstein, David, Hadi, Masood Z., Hellsten, Uffe, Hildebrand, Mark, Jenkins, Bethany D., Jurka, Jerzy, Kapitonov, Vladimir V., Kröger, Nils, Lane, Todd W., Larimer, Frank W., Lippmeier, J. Casey, Lucas, Susan, Medina, Mónica, Montsant, Anton, Obornik, Miroslav, Parker, Micaela Schnitzler, Palenik, Brian, Pazour, Gregory J., Richardson, Paul M., Rynearson, Tatiana A., Saito, Mak A., Schwartz, David C., Thamatrakoln, Kimberlee, Valentin, Klaus, Vardi, Assaf, Wilkerson, Frances P., and Rokhsar, Daniel S.

Published
2004

3. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).

Author

Clum, Alicia, Tindall, Brian J, Sikorski, Johannes, Ivanova, Natalia, Mavrommatis, Konstantinos, Lucas, Susan, Glavina, Tijana, Del Rio, Nolan, Matt, Chen, Feng, Tice, Hope, Pitluck, Sam, Cheng, Jan-Fang, Chertkov, Olga, Brettin, Thomas, Han, Cliff, Detter, John C, Kuske, Cheryl, Bruce, David, Goodwin, Lynne, Ovchinikova, Galina, Pati, Amrita, Mikhailova, Natalia, Chen, Amy, Palaniappan, Krishna, Land, Miriam, Hauser, Loren, Chang, Yun-Juan, Jeffries, Cynthia D, Chain, Patrick, Rohde, Manfred, Göker, Markus, Bristow, Jim, Eisen, Jonathan A, Markowitz, Victor, Hugenholtz, Philip, Kyrpides, Nikos C, Klenk, Hans-Peter, and Lapidus, Alla

Subjects
GEBA, Gram-negative, Planctomycetaceae, developmental life cycle, mesophile, prosthecate budding bacteria, ‘Planctomycetes’, non-prosthecate budding bacteria, 'Planctomycetes', Human Genome, Biotechnology, Genetics, Biochemistry and Cell Biology
Abstract

Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

Published
2009

4. The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

Author

Challacombe, Jean F., Altherr, Michael R., Xie, Gary, Bhotika, Smriti S., Brown, Nancy, Bruce, David, Campbell, Connie S., Campbell, Mary L., Chen, Jin, Chertkov, Olga, Cleland, Cathy, Dimitrijevic, Mira, Doggett, Norman A., Fawcett, John J., Glavina, Tijana, Goodwin, Lynne A., Green, Lance D., Han, Cliff S., Hill, Karen K., Hitchcock, Penny, Jackson, Paul J., Keim, Paul, Kewalramani, Avinash Ramesh, Longmire, Jon, Lucas, Susan, Malfatti, Stephanie, Martinez, Diego, McMurry, Kim, Meincke, Linda J., Misra, Monica, Moseman, Bernice L., Mundt, Mark, Munk, A. Christine, Okinaka, Richard T., Parson-Quintana, B., Reilly, Lee Philip, Richardson, Paul, Robinson, Donna L., Rubin, Eddy, Saunders, Elizabeth, Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Ticknor, Lawrence O., Wills, Patti L., Gilna, Paul, and Brettin, Thomas S.

Subjects
Basic biological sciences
Abstract

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (3). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (2).

Published
2008

5. The Draft Genome of Ciona intestinalis: Insights into Chordate and Vertebrate Origins

Author

Dehal, Paramvir, Satou, Yutaka, Campbell, Robert K., Chapman, Jarrod, Degnan, Bernard, de Tomaso, Anthony, Davidson, Brad, Di Gregorio, Anna, Gelpke, Maarten, Goodstein, David M., Harafuji, Naoe, Ho, Isaac, Hotta, Kohji, Huang, Wayne, Kawashima, Takeshi, Lemaire, Patrick, Martinez, Diego, Meinertzhagen, Ian A., Necula, Simona, Nonaka, Masaru, Putnam, Nik, Rash, Sam, Saiga, Hidetoshi, Satake, Masanobu, Terry, Astrid, Yamada, Lixy, Wang, Hong-Gang, Awazu, Satoko, Azumi, Kaoru, Boore, Jeffrey, Branno, Margherita, Chin-bow, Stephen, DeSantis, Rosaria, Doyle, Sharon, Francino, Pilar, Keys, David N., Haga, Shinobu, Hayashi, Hiroko, Hino, Kyosuke, Imai, Kaoru S., Inaba, Kazuo, Kano, Shungo, Kobayashi, Kenji, Kobayashi, Mari, Lee, Byung-In, Makabe, Kazuhiro W., Manohar, Chitra, Matassi, Giorgio, Medina, Monica, Mochizuki, Yasuaki, Mount, Steve, Morishita, Tomomi, Miura, Sachiko, Nakayama, Akie, Nishizaka, Satoko, Nomoto, Hisayo, Ohta, Fumiko, Oishi, Kazuko, Rigoutsos, Isidore, Sano, Masako, Sasaki, Akane, Sasakura, Yasunori, Shoguchi, Eiichi, Spagnuolo, Antoinetta, Stainier, Didier, Suzuki, Miho M., Tassy, Olivier, Takatori, Naohito, Tokuoka, Miki, Yagi, Kasumi, Yoshizaki, Fumiko, Wada, Shuichi, Zhang, Cindy, Hyatt, P. Douglas, Larimer, Frank, Detter, Chris, Doggett, Norman, Glavina, Tijana, Hawkins, Trevor, Richardson, Paul, Lucas, Susan, Kohara, Yuji, Levine, Michael, Satoh, Nori, and Rokhsar, Daniel S.

Published
2002

6. The Pathogenomic Sequence Analysis of B. cereus and B. thuringiensis Isolates Closely Related to Bacillus anthracis

Author

Han, Cliff S., Xie, Gary, Challacombe, Jean F., Altherr, Michael R., Smriti, B., Bruce, David, Campbell, Connie S., Campbell, Mary L., Chen, Jin, Chertkov, Olga, Cleland, Cathy, Dimitrijevic-Bussod, M., Doggett, Norman A., Fawcett, John J., Glavina, Tijana, Goodwin, Lynne A., Hill, Karen K., Hitchcock, Penny, Jackson, Paul J., Keim, Paul, Kewalramani, Avinash Ramesh, Longmire, Jon, Lucas, Susan, Malfatti, Stephanie, McMurry, Kim, Meincke, Linda J., Misra, Monica, Moseman, Bernice L., Mundt, Mark, Munk, A. Christine, Okinaka, Richard T., Parson-Quintana, B., Reilly, Lee P., Richardson, Paul, Robinson, Donna L., Rubin, Eddy, Saunders, Elizabeth, Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Ticknor, Lawrence O., Wills, Patti L., Gilna, Payl, and Brettin, Thomas S.

Subjects
Basic biological sciences, Comparative analysis genomics evolution virulence opportunistic pathogen
Abstract

The sequencing and analysis of two close relatives of Bacillus anthracis are reported. AFLP analysis of over 300 isolates of B. cereus, B. thuringiensis and B. anthracis identified two isolates as being very closely related to B. anthracis. One, a B. cereus, BcE33L, was isolated from a zebra carcass in Nambia; the second, a B. thuringiensis, 97-27, was isolated from a necrotic human wound. The B. cereus appears to be the closest anthracis relative sequenced to date. A core genome of over 3,900 genes was compiled for the Bacillus cereus group, including B anthracis. Comparative analysis of these two genomes with other members of the B. cereus group provides insight into the evolutionary relationships among these organisms. Evidence is presented that differential regulation modulates virulence, rather than simple acquisition of virulence factors. These genome sequences provide insight into the molecular mechanisms contributing to the host range and virulence of this group of organisms.

Published
2005

7. Advancements in the DOE Joint Genome Institute's High Throughput Production Sequencing Program

Author

Lucas, Susan M., Detter, John C., Glavina, Tijana, Hammon, Nancy, Israni, Sanjay, Pollard, Martin, Copeland, Alex, Barry, Kerrie, Roberts, Simon, Chen, Feng, Slater, Nathaniel, Pitluck, Samuel, Daum, Christopher, Richardson, Paul, and Rubin, Eddy

Abstract

Advancements in the DOE Joint Genome Institute's High Throughput Production Sequencing Program Susan M. Lucas, John C. Detter , Tijana Glavina, Nancy Hammon, Sanjay Israni, Martin Pollard, Alex Copeland, Kerrie Barry, Simon Roberts, Feng Chen, Nathaniel Slater, Samuel Pitluck, Christopher Daum, Paul Richardson, Eddy Rubin, and the JGI Sequencing TeamU.S. DOE Joint Genome Institute, Walnut Creek, CA 94598 The Department of Energy s (DOE) Joint Genome Institute (JGI) Production Genomics Facility (PGF) is responsible for high throughput sequencing. The sequencing process is divided into three subgroups; Library Support, Sequencing Prep and Capillary Electrophoresis, which collectively transform a variety of input DNAs into high quality shotgun sequence. Transformation stocks from whole genome shotgun libraries enter the process at the Library Support step, where they are plated, picked and the 3kb and 8kb libraries are sent on for template preparation using Templiphi. Fosmid DNA is prepared in parallel using the SPRInt protocol from Agencourt. Clones are then end sequenced using Big Dye Terminator or Dyenamic ET chemistry kits and run on their respective platforms ABI 3730xl or MegaBACE 4000. A series of automated post-sequencing data processing steps then convert the raw shotgun sequence into assembled contigs, where the data is QC d and prepared for release. In our efforts to scale production over the last year, the process has undergone dynamic changes to increase throughput and efficiency. Changes have occurred in sequencing chemistry to both reduce cost as well as generate high quality sequence for GC-rich templates. Tracking efficiency has increased due to the release of a new LIMS. The implementation of a training program and preventative maintenance program has allowed for stability of both instruments and staff. The conversion of the MegaBACE 4000 to the MegaBACE 4500 has had a direct effect on increased readlenths and pass rates. In combination, all of these changes have resulted in significant improvements in pass rates, readlengths, stability and cost savings, enabling the PGF to put through several large sequencing projects through including Xenopus tropicalis, Nematostella vectensis, Emiliania huxyeli, and over fifty microbes, maintaining a monthly throughput of 3.9 million lanes resulting in ~2.4 billion Q20 base pairs. This work was performed under the auspices of the U.S. Department of Energy, Office of Biological and Environmental Research, by the University of California, Lawrence Livermore National Laboratory under Contract No. W-7405-Eng-48, the Lawrence Berkeley National Laboratory under contract No. DE-AC03-76SF00098, and the Los Alamos National Laboratory under contract No. W-7405-ENG-36.

Published
2005

8. The US DOE Joint Genome Institute Microbial Genome Program

Author

Lapidus, Alla, Chain, Patrick, Han, Cliff, Brettin, Thomas, Copeland, Alex, Barry, Kerrie, Detter, J. Chris, Glavina, Tijana, Lucas, Susan, Land, Miriam, Larimer, Frank, Kyrpides, Nikos, Ivanova, Natalia, Schmutz, Jeremy, Markowitz, Victor M., Bruce, David, Gilna, Paul, Bristow, Jim, Rubin, Eddy, and Richardson, Paul M.

Subjects
Microbial Genome Program
Published
2005

9. Creating Custom Software for the Genetix QPixII Colony Picker using the Genetix Developer's Toolkit SDK

Author

Wilson, Steven, Radding, Zach, Glavina, Tijana, Hesse, Jennifer, Huynh, Sandy, Mihalkanin, Danielle, and Pollard, Martin

Abstract

Developing Custom Picking Software Using the Genetix SDK Presenting Author: Steven E. Wilson U.S. DOE Joint Genome Institute2800 Mitchell Drive, Bldg. 100 Walnut Creek, CA 94598 sewilson@lbl.gov(925) 296-5769 Automated colony picking has allowed DOE s Joint Genome Institute to inoculate upwards of 215 384-well plates per day. JGI currently attains a ratio of about 2.5 destination plates per bioassay tray (~1000 colonies per bioassay tray) and 2 or fewer failed wells per plate. The picking setup screen can also be overwhelming for new users that do not know how to navigate the user interface.The Genetix software developer s toolkit (SDK) allows programmers to create imaging and picking routines that suite the specific needs of their clients. The JGI has taken advantage of the SDK by creating a program that shows the machine operators only what they need to see on a plate to plate basis, uses a special calibration routine and implementing a background subtraction routine that increases the contrast between the agar media and the colonies. Used together, the JGI will stabilize the number of failed wells and increase the number of colonies that are imaged per bioassay tray. With the implementation of the custom software, JGI hopes to reduce reagent and plastics costs, increase picking efficiency and streamline the picking process.

Published
2005

12. The sequence and analysis of duplication rich human chromosome 16

Author

Martin, Joel, Han, Cliff, Gordon, Laurie A., Terry, Astrid, Prabhakar, Shyam, She, Xinwei, Xie, Gary, Hellsten, Uffe, Man Chan, Yee, Altherr, Michael, Couronne, Olivier, Aerts, Andrea, Bajorek, Eva, Black, Stacey, Blumer, Heather, Branscomb, Elbert, Brown, Nancy C., Bruno, William J., Buckingham, Judith M., Callen, David F., Campbell, Connie S., Campbell, Mary L., Campbell, Evelyn W., Caoile, Chenier, Challacombe, Jean F., Chasteen, Leslie A., Chertkov, Olga, Chi, Han C., Christensen, Mari, Clark, Lynn M., Cohn, Judith D., Denys, Mirian, Detter, John C., Dickson, Mark, Dimitrijevic-Bussod, Mira, Escobar, Julio, Fawcett, Joseph J., Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Goodwin, Lynne A., Grady, Deborah L., Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Hildebrand, Carl E., Huang, Wayne, Israni, Sanjay, Jett, Jamie, Jewett, Phillip E., Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Krawczyk, Marie-Claude, Leyba, Tina, Longmire, Jonathan L., Lopez, Frederick, Lou, Yunian, Lowry, Steve, Ludeman, Thom, Mark, Graham A., Mcmurray, Kimberly L., Meincke, Linda J., Morgan, Jenna, Moyzis, Robert K., Mundt, Mark O., Munk, A. Christine, Nandkeshwar, Richard D., Pitluck, Sam, Pollard, Martin, Predki, Paul, Parson-Quintana, Beverly, Ramirez, Lucia, Rash, Sam, Retterer, James, Ricke, Darryl O., Robinson, Donna L., Rodriguez, Alex, Salamov, Asaf, Saunders, Elizabeth H., Scott, Duncan, Shough, Timothy, Stallings, Raymond L., Stalvey, Malinda, Sutherland, Robert D., Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Torney, David C., Tran-Gyamfi, Mary, Tsai, Ming, Ulanovsky, Levy E., and Ustaszewska, Anna

Subjects
Applied life sciences
Abstract

We report here the 78,884,754 base pairs of finished human chromosome 16 sequence, representing over 99.9 percent of its euchromatin. Manual annotation revealed 880 protein coding genes confirmed by 1,637 aligned transcripts, 19 tRNA genes, 341 pseudogenes and 3 RNA pseudogenes. These genes include metallothionein, cadherin and iroquois gene families, as well as the disease genes for polycystic kidney disease and acute myelomonocytic leukemia. Several large-scale structural polymorphisms spanning hundreds of kilobasepairs were identified and result in gene content differences across humans. One of the unique features of chromosome 16 is its high level of segmental duplication, ranked among the highest of the human autosomes. While the segmental duplications are enriched in the relatively gene poor pericentromere of the p-arm, some are involved in recent gene duplication and conversion events which are likely to have had an impact on the evolution of primates and human disease susceptibility.

Published
2004

13. The complete sequence of human chromosome 5

Author

Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, State, Gordon, Laurie A., Scott, Duncan, Xie, Gary, Huang, Wayne, Hellsten, Uffe, Tran-Gyamfi, Mary, She, Xinwei, Prabhakar, Shyam, Aerts, Andrea, Altherr, Michael, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caoile, Chenier, Challacombe, Jean F., Chan, Yee Man, Denys, Mirian, Detter, Chris, Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstenin, David, Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimbal, Heather, Kobayashi, Arthur, Lopez, Frederick, Lou, Yunian, Martinez, Diego, Medina, Catherine, Morgan, Jenna, Nandkeshwar, Richard, Noonan, James P., Pitluck, Sam, Pollard, Martin, Predki, Paul, Priest, James, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanie, Salamov, Asaf, Salazar, Angelica, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wheeler, Jeremy, Wu, Kevin, Yang, Joan, Dickson, Mark, Cheng, Jan-Fang, Eichler, Evan E., Olsen, Anne, Pennacchio, Len A., Rokhsar, Daniel S., Richardson, Paul, Lucas, Susan M., Myers, Richard M., and Rubin, Edward M.

Subjects
Applied life sciences
Abstract

Chromosome 5 is one of the largest human chromosomes yet has one of the lowest gene densities. This is partially explained by numerous gene-poor regions that display a remarkable degree of noncoding and syntenic conservation with non-mammalian vertebrates, suggesting they are functionally constrained. In total, we compiled 177.7 million base pairs of highly accurate finished sequence containing 923 manually curated protein-encoding genes including the protocadherin and interleukin gene families and the first complete versions of each of the large chromosome 5 specific internal duplications. These duplications are very recent evolutionary events and play a likely mechanistic role, since deletions of these regions are the cause of debilitating disorders including spinal muscular atrophy (SMA).

Published
2004

14. Mechanisms of thermal adaptation revealed from the genomes of the Anta rctic and

Author

Saunders, Neil F.W., Thomas, Torsten, Curmi, Paul M.G., Mattick, John S., Kuczek, Elizabeth, Slade, Rob, Davis, John, Franzmann, Peter, Boone, David, Rusterholtz, Karl, Feldman, Robert, Gates, Chris, Bench, Shellie, Sowers, Kevin, Kadner, Kristen, Aerts, Andrea, Dehal, Paramvir, Detter, Chris, Glavina, Tijana, Lucas, Susan, Richardson, Paul, Larimer, Frank, Hauser, Frank, Hauser, Loren, Land, Miriam, and Cavicchioli, Richard

Subjects
Genomes of the Antarctic Archaea Methanogenium frididum and Methanococcoides burtonii
Abstract

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 non-charged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15-98oC) was used to generate 1 111 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 an 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 60oC, 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.

Published
2003

15. Pathogenomic sequence analysis of Bacillus cereus and Bacillus thuringiensis isolates closely related to Bacillus anthracis

Author

Han, Cliff S., Xie, Gary, Challacombe, Jean F., Altherr, Michael R., Bhotika, Smriti S., Bruce, David, Campbell, Connie S., Campbell, Mary L., Chen, Jin, Chertkov, Olga, Cleland, Cathy, Dimitrijevic, Mira, Doggett, Norman A., Fawcett, John J., Glavina, Tijana, Goodwin, Lynne A., Hill, Karen K., Hitchcock, Penny, Jackson, Paul J., Keim, Paul, Kewalramani, Avinash Ramesh, Longmire, Jon, Lucas, Susan, Malfatti, Stephanie, McMurry, Kim, Meincke, Linda J., Misra, Monica, Moseman, Bernice L., Mundt, Mark, Munk, A. Christine, Okinaka, Richard T., Parson-Quintana, B., Reilly, Lee Philip, Richardson, Paul, Robinson, Donna L., Rubin, Eddy, Saunders, Elizabeth, Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Ticknor, Lawrence O., Wills, Patti L., Brettin, Thomas S., and Gilna, Paul

Subjects
Bacillus cereus -- Environmental aspects, Bacillus cereus -- Genetic aspects, Bacillus thuringiensis -- Environmental aspects, Bacillus thuringiensis -- Genetic aspects, Bacillus anthracis -- Environmental aspects, Bacillus anthracis -- Genetic aspects, Genetic research, Biological sciences
Abstract

Bacillus anthracis, Bacillus cereus, and Bacillus thuringiensis are closely related gram-positive, spore-forming bacteria of the B. cereus sensu lato group. While independently derived strains of B. anthracis reveal conspicuous sequence homogeneity, environmental isolates of B. cereus and B. thuringiensis exhibit extensive genetic diversity. Here we report the sequencing and comparative analysis of the genomes of two members of the B. cereus group, B. thuringiensis 97-27 subsp, konkukian serotype H34, isolated from a necrotic human wound, and B. cereus E33L, which was isolated from a swab of a zebra carcass in Namibia. These two strains, when analyzed by amplified fragment length polymorphism within a collection of over 300 of B. cereus, B. thuringiensis, and B. anthracis isolates, appear closely related to B. anthracis. The B. cereus E33L isolate appears to be the nearest relative to B. anthracis identified thus far. Whole-genome sequencing of B. thuringiensis 97-27 and B. cereus E33L was undertaken to identify shared and unique genes among these isolates in comparison to the genomes of pathogenic strains B. anthracis Ames and B. cereus G9241 and nonpathogenic strains B. cereus ATCC 10987 and B. cereus ATCC 14579. Comparison of these genomes revealed differences in terms of virulence, metabolic competence, structural components, and regulatory mechanisms.

Published
2006

16. The DNA sequence and biology of human chromosome 19

Author

Grimwood, Jane, Gordon, Laurie A., Olsen, Anne, Terry, Astrid, Schmutz, Jeremy, Lamerdin, Jane, Hellsten, Uffe, Goodstein, David, Couronne, Olivier, Tran-Gyamfi, Mary, Aerts, Andrea, Altherr, Michael, Ashworth, Linda, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caenepeel, Sean, Carrano, Anthony, Caoile, Chenier, Man Chan, Yee, Christensen, Mari, Cleland, Catherine A., Copeland, Alex, Dalin, Eileen, Dehal, Paramvir, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Garcia, Carmen, Georgescu, Anca M., Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Ho, Isaac, Huang, Wayne, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Larionov, Vladimer, Leem, Sun-Hee, Lopez, Frederick, Lou, Yunian, Lowry, Steve, Malfatti, Stephanie, Martinez, Diego, McCready, Paula, Medina, Catherine, Morgan, Jenna, Nelson, Kathryn, Nolan, Matt, Ovcharenko, Ivan, Pitluck, Sam, Pollard, Martin, Popkie, Anthony P., Predki, Paul, Quan, Glenda, Ramirez, Lucia, Rash, Sam, Retterer, James, Rodriguez, Alex, Rogers, Stephanine, Salamov, Asaf, Salazar, Angelica, She, Xinwei, Smith, Doug, Slezak, Tom, Solovyev, Victor, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wagner, Mark, Wheeler, Jeremy, Wu, Kevin, Xie, Gary, Yang, Joan, Dubchak, Inna, Furey, Terrence S., DeJong, Pieter, Dickson, Mark, Gordon, David, Eichler, Evan E., Pennacchio, Len A., Richardson, Paul, Stubbs, Lisa, Rokhsar, Daniel S., Myers, Richard M., Rubin, Edward M., and Lucas, Susan M.

Published
2004
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17. The DNA sequence and comparative analysis of human chromosome 5

Author

Schmutz, Jeremy, Martin, Joel, Terry, Astrid, Couronne, Olivier, Grimwood, Jane, Lowry, Steve, Gordon, Laurie A., Scott, Duncan, Xie, Gary, Huang, Wayne, Hellsten, Uffe, Tran-Gyamfi, Mary, She, Xinwei, Prabhakar, Shyam, Aerts, Andrea, Altherr, Michael, Bajorek, Eva, Black, Stacey, Branscomb, Elbert, Caoile, Chenier, Challacombe, Jean F., Man Chan, Yee, Denys, Mirian, Detter, John C., Escobar, Julio, Flowers, Dave, Fotopulos, Dea, Glavina, Tijana, Gomez, Maria, Gonzales, Eidelyn, Goodstein, David, Grigoriev, Igor, Groza, Matthew, Hammon, Nancy, Hawkins, Trevor, Haydu, Lauren, Israni, Sanjay, Jett, Jamie, Kadner, Kristen, Kimball, Heather, Kobayashi, Arthur, Lopez, Frederick, Lou, Yunian, Martinez, Diego, Medina, Catherine, Morgan, Jenna, Nandkeshwar, Richard, Noonan, James P., Pitluck, Sam, Pollard, Martin, Predki, Paul, Priest, James, Ramirez, Lucia, Retterer, James, Rodriguez, Alex, Rogers, Stephanie, Salamov, Asaf, Salazar, Angelica, Thayer, Nina, Tice, Hope, Tsai, Ming, Ustaszewska, Anna, Vo, Nu, Wheeler, Jeremy, Wu, Kevin, Yang, Joan, Dickson, Mark, Cheng, Jan-Fang, Eichler, Evan E., Olsen, Anne, Pennacchio, Len A., Rokhsar, Daniel S., Richardson, Paul, Lucas, Susan M., Myers, Richard M., and Rubin, Edward M.

Subjects
Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Author(s): Jeremy Schmutz (corresponding author) [1]; Joel Martin [2]; Astrid Terry [2]; Olivier Couronne [3]; Jane Grimwood [1]; Steve Lowry [2]; Laurie A. Gordon [2, 4]; Duncan Scott [2]; Gary [...]

Published
2004
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18. Closing the gaps on human chromosome 19 revealed genes with a high density of repetitive tandemly arrayed elements

Author

Leem, Sun-Hee, Kouprina, Natalay, Grimwood, Jane, Kim, Jung-Hyun, Mullokandov, Michael, Yoon, Young-Ho, Chae, Ji-Youn, Morgan, Jenna, Lucas, Susan, Larionov, Vladimir, Barrett, Carl J., Rubbin, Eddy, Glavina, Tijana, Detter, Chris, and Richardson, Paul

Subjects
Human cloning -- Research, Human genetics -- Research, Human chromosomes -- Research, Genetic research, Health
Abstract

The transformation-associated recombination (TAR) cloning approach and screening of additional genomic libraries are used to close gaps on human chromosome 19. It is found that the use of the alternative recombinational cloning system in yeast may greatly accelerate the process of closing the gaps in the human genome to achieve the goal of annotation of all human genes.

Published
2004

19. The complete genome sequence of Bacillus thuringiensis Al Hakam

Author

Challacombe, Jean F., Altherr, Michael R., Xie, Gary, Bhotika, Smriti S., Brown, Nancy, Bruce, David, Campbell, Connie S., Campbell, Mary L., Chen, Jin, Chertkov, Olga, Cleland, Cathy, Dimitrijevic, Mira, Doggett, Norman A., Fawcett, John J., Glavina, Tijana, Goodwin, Lynne A., Green, Lance D., Han, Cliff S., Hill, Karen K., Hitchcock, Penny, Jackson, Paul J., Keim, Paul, Kewalramani, Avinash Ramesh, Longmire, Jon, Lucas, Susan, Malfatti, Stephanie, Martinez, Diego, McMurry, Kim, Meincke, Linda J., Misra, Monica, Moseman, Bernice L., Mundt, Mark, Munk, A. Christine, Okinaka, Richard T., Parson-Quintana, B., Reilly, Lee Philip, Richardson, Paul, Robinson, Donna L., Saunders, Elizabeth, Tapia, Roxanne, Tesmer, Judith G., Thayer, Nina, Thompson, Linda S., Tice, Hope, Ticknor, Lawrence O., Wills, Patti L., Gilna, Paul, and Brettin, Thomas S.

Subjects
Bacillus thuringiensis -- Genetic aspects, Bacillus thuringiensis -- Research, Genomes -- Research, Biological sciences
Abstract

Bacillus thuringiensis is an insect pathogen that is widely used as a biopesticide (E. Schnepf, N. Crickmore, J. Van Rie, D. Lereclus, J. Baum, J. Feitelson, D. R. Zeigler, and D. H. Dean, Microbiol. Mol. Biol. Rev. 62:775-806, 1998). Here we report the finished, annotated genome sequence of B. thuringiensis Al Hakam, which was collected in Iraq by the United Nations Special Commission (L. Radnedge, P. Agron, K. Hill, P. Jackson, L. Ticknor, P. Keim, and G. Andersen, Appl. Environ. Microbiol. 69:2755-2764, 2003). doi:10.1128/JB.00241-07

Published
2007

20. Mechanisms of thermal adaptation revealed from the genomes of the Anta rctic <italic Archaea, Methanogenium frigidum > and <italic Methanococcoides burtonii >

Author

Saunders, Neil F.W., Thomas, Torsten, Curmi, Paul M.G., Mattick, John S., Kuczek, Elizabeth, Slade, Rob, Davis, John, Franzmann, Peter, Boone, David, Rusterholtz, Karl, Feldman, Robert, Gates, Chris, Bench, Shellie, Sowers, Kevin, Kadner, Kristen, Aerts, Andrea, Dehal, Paramvir, Detter, Chris, Glavina, Tijana, Lucas, Susan, Richardson, Paul, Larimer, Frank, Hauser, Frank, Hauser, Loren, Land, Miriam, and Cavicchioli, Richard

Subjects
Genomes of the Antarctic Archaea Methanogenium frididum and Methanococcoides burtonii
Abstract

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 non-charged polar amino acids, particularly Gln and Thr and a lower content of hydrophobic amino acids, particularly Leu. Sequence data from nine methanogen genomes (OGT 15-98oC) was used to generate 1 111 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 an 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 60oC, 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.

Published
2003

21. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Author

Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, Yang, Huanming, Wong, Gane Ka-Shu, Liu, Bin, Wang, Jun, Zhang, Yong, Yang, Xu, Zhang, Zengjin, Meng, Qingshun, Zhou, Jun, Li, Dawei, Zhang, Jingjing, Ni, Peixiang, Li, Songgang, Ran, Longhua, Li, Heng, Zhang, Jianguo, Li, Ruiqiang, Li, Shengting, Zheng, Hongkun, Lin, Wei, Li, Guangyuan, Wang, Xiaoling, Zhao, Wenming, Li, Jun, Ye, Chen, Dai, Mingtao, Ruan, Jue, Zhou, Yan, Li, Yuanzhe, He, Ximiao, Zhang, Yunze, Wang, Jing, Huang, Xiangang, Tong, Wei, Chen, Jie, Ye, Jia, Chen, Chen, Wei, Ning, Li, Guoqing, Dong, Le, Lan, Fengdi, Sun, Yongqiao, Zhang, Zhenpeng, Yang, Zheng, Yu, Yingpu, Huang, Yanqing, He, Dandan, Xi, Yan, Wei, Dong, Qi, Qiuhui, Li, Wenjie, Shi, Jianping, Wang, Miaoheng, Xie, Fei, Wang, Jianjun, Zhang, Xiaowei, Wang, Pei, Zhao, Yiqiang, Li, Ning, Yang, Ning, Dong, Wei, Hu, Songnian, Zeng, Changqing, Zheng, Weimou, Hao, Bailin, Hillier, Ladeana W, Yang, Shiaw-Pyng, Warren, Wesley C, Wilson, Richard K, Brandström, Mikael, Ellegren, Hans, Crooijmans, Richard P M A, van der Poel, Jan J, Bovenhuis, Henk, Groenen, Martien A M, Ovcharenko, Ivan, Gordon, Laurie, Stubbs, Lisa, Lucas, Susan, Glavina, Tijana, Aerts, Andrea, Kaiser, Pete, Rothwell, Lisa, Young, John R, Rogers, Sally, Walker, Brian A, van Hateren, Andy, Kaufman, Jim, Bumstead, Nat, Lamont, Susan J, Zhou, Huaijun, Hocking, Paul M, Morrice, David, de Koning, Dirk-Jan, Law, Andy, Bartley, Neil, Burt, David W, Hunt, Henry, Cheng, Hans H, Gunnarsson, Ulrika, Wahlberg, Per, Andersson, Leif, Kindlund, Ellen, Tammi, Martti T, Andersson, Björn, Webber, Caleb, Ponting, Chris P, Overton, Ian M, Boardman, Paul E, Tang, Haizhou, Hubbard, Simon J, Wilson, Stuart A, Yu, Jun, Wang, Jian, and Yang, Huanming

Published
2004

22. The sequence and analysis of duplication-rich human chromosome 16

Author

Martin, Joel, primary, Han, Cliff, additional, Gordon, Laurie A., additional, Terry, Astrid, additional, Prabhakar, Shyam, additional, She, Xinwei, additional, Xie, Gary, additional, Hellsten, Uffe, additional, Chan, Yee Man, additional, Altherr, Michael, additional, Couronne, Olivier, additional, Aerts, Andrea, additional, Bajorek, Eva, additional, Black, Stacey, additional, Blumer, Heather, additional, Branscomb, Elbert, additional, Brown, Nancy C., additional, Bruno, William J., additional, Buckingham, Judith M., additional, Callen, David F., additional, Campbell, Connie S., additional, Campbell, Mary L., additional, Campbell, Evelyn W., additional, Caoile, Chenier, additional, Challacombe, Jean F., additional, Chasteen, Leslie A., additional, Chertkov, Olga, additional, Chi, Han C., additional, Christensen, Mari, additional, Clark, Lynn M., additional, Cohn, Judith D., additional, Denys, Mirian, additional, Detter, John C., additional, Dickson, Mark, additional, Dimitrijevic-Bussod, Mira, additional, Escobar, Julio, additional, Fawcett, Joseph J., additional, Flowers, Dave, additional, Fotopulos, Dea, additional, Glavina, Tijana, additional, Gomez, Maria, additional, Gonzales, Eidelyn, additional, Goodstein, David, additional, Goodwin, Lynne A., additional, Grady, Deborah L., additional, Grigoriev, Igor, additional, Groza, Matthew, additional, Hammon, Nancy, additional, Hawkins, Trevor, additional, Haydu, Lauren, additional, Hildebrand, Carl E., additional, Huang, Wayne, additional, Israni, Sanjay, additional, Jett, Jamie, additional, Jewett, Phillip B., additional, Kadner, Kristen, additional, Kimball, Heather, additional, Kobayashi, Arthur, additional, Krawczyk, Marie-Claude, additional, Leyba, Tina, additional, Longmire, Jonathan L., additional, Lopez, Frederick, additional, Lou, Yunian, additional, Lowry, Steve, additional, Ludeman, Thom, additional, Manohar, Chitra F., additional, Mark, Graham A., additional, McMurray, Kimberly L., additional, Meincke, Linda J., additional, Morgan, Jenna, additional, Moyzis, Robert K., additional, Mundt, Mark O., additional, Munk, A. Christine, additional, Nandkeshwar, Richard D., additional, Pitluck, Sam, additional, Pollard, Martin, additional, Predki, Paul, additional, Parson-Quintana, Beverly, additional, Ramirez, Lucia, additional, Rash, Sam, additional, Retterer, James, additional, Ricke, Darryl O., additional, Robinson, Donna L., additional, Rodriguez, Alex, additional, Salamov, Asaf, additional, Saunders, Elizabeth H., additional, Scott, Duncan, additional, Shough, Timothy, additional, Stallings, Raymond L., additional, Stalvey, Malinda, additional, Sutherland, Robert D., additional, Tapia, Roxanne, additional, Tesmer, Judith G., additional, Thayer, Nina, additional, Thompson, Linda S., additional, Tice, Hope, additional, Torney, David C., additional, Tran-Gyamfi, Mary, additional, Tsai, Ming, additional, Ulanovsky, Levy E., additional, Ustaszewska, Anna, additional, Vo, Nu, additional, Scott White, P., additional, Williams, Albert L., additional, Wills, Patricia L., additional, Wu, Jung-Rung, additional, Wu, Kevin, additional, Yang, Joan, additional, DeJong, Pieter, additional, Bruce, David, additional, Doggett, Norman A., additional, Deaven, Larry, additional, Schmutz, Jeremy, additional, Grimwood, Jane, additional, Richardson, Paul, additional, Rokhsar, Daniel S., additional, Eichler, Evan E., additional, Gilna, Paul, additional, Lucas, Susan M., additional, Myers, Richard M., additional, Rubin, Edward M., additional, and Pennacchio, Len A., additional

Published
2004
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23. Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii

Author

Saunders, Neil F.W., primary, Thomas, Torsten, additional, Curmi, Paul M.G., additional, Mattick, John S., additional, Kuczek, Elizabeth, additional, Slade, Rob, additional, Davis, John, additional, Franzmann, Peter D., additional, Boone, David, additional, Rusterholtz, Karl, additional, Feldman, Robert, additional, Gates, Chris, additional, Bench, Shellie, additional, Sowers, Kevin, additional, Kadner, Kristen, additional, Aerts, Andrea, additional, Dehal, Paramvir, additional, Detter, Chris, additional, Glavina, Tijana, additional, Lucas, Susan, additional, Richardson, Paul, additional, Larimer, Frank, additional, Hauser, Loren, additional, Land, Miriam, additional, and Cavicchioli, Ricardo, additional

Published
2003
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26. A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms.

Author

Wong GK, Liu B, Wang J, Zhang Y, Yang X, Zhang Z, Meng Q, Zhou J, Li D, Zhang J, Ni P, Li S, Ran L, Li H, Zhang J, Li R, Li S, Zheng H, Lin W, Li G, Wang X, Zhao W, Li J, Ye C, Dai M, Ruan J, Zhou Y, Li Y, He X, Zhang Y, Wang J, Huang X, Tong W, Chen J, Ye J, Chen C, Wei N, Li G, Dong L, Lan F, Sun Y, Zhang Z, Yang Z, Yu Y, Huang Y, He D, Xi Y, Wei D, Qi Q, Li W, Shi J, Wang M, Xie F, Wang J, Zhang X, Wang P, Zhao Y, Li N, Yang N, Dong W, Hu S, Zeng C, Zheng W, Hao B, Hillier LW, Yang SP, Warren WC, Wilson RK, Brandström M, Ellegren H, Crooijmans RP, van der Poel JJ, Bovenhuis H, Groenen MA, Ovcharenko I, Gordon L, Stubbs L, Lucas S, Glavina T, Aerts A, Kaiser P, Rothwell L, Young JR, Rogers S, Walker BA, van Hateren A, Kaufman J, Bumstead N, Lamont SJ, Zhou H, Hocking PM, Morrice D, de Koning DJ, Law A, Bartley N, Burt DW, Hunt H, Cheng HH, Gunnarsson U, Wahlberg P, Andersson L, Kindlund E, Tammi MT, Andersson B, Webber C, Ponting CP, Overton IM, Boardman PE, Tang H, Hubbard SJ, Wilson SA, Yu J, Wang J, and Yang H

Subjects
Alleles, Amino Acid Sequence, Animals, Animals, Domestic classification, Animals, Domestic genetics, Chickens classification, Chromosomes genetics, Female, Haplotypes genetics, Humans, Molecular Sequence Data, Ornithine Carbamoyltransferase chemistry, Selection, Genetic, Chickens genetics, Genome, Genomics, Physical Chromosome Mapping, Polymorphism, Single Nucleotide genetics
Abstract

We describe a genetic variation map for the chicken genome containing 2.8 million single-nucleotide polymorphisms (SNPs). This map is based on a comparison of the sequences of three domestic chicken breeds (a broiler, a layer and a Chinese silkie) with that of their wild ancestor, red jungle fowl. Subsequent experiments indicate that at least 90% of the variant sites are true SNPs, and at least 70% are common SNPs that segregate in many domestic breeds. Mean nucleotide diversity is about five SNPs per kilobase for almost every possible comparison between red jungle fowl and domestic lines, between two different domestic lines, and within domestic lines--in contrast to the notion that domestic animals are highly inbred relative to their wild ancestors. In fact, most of the SNPs originated before domestication, and there is little evidence of selective sweeps for adaptive alleles on length scales greater than 100 kilobases.

Published
2004
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