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23 results on '"Glavina, Tijana"'

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

Author

Liolios, Konstantinos, 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, Kyrpides, Nikos C, Liolios, Konstantinos, 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

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

Author

Liolios, Konstantinos, 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, Kyrpides, Nikos C, Liolios, Konstantinos, 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

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

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

Author

Clum, Alicia, 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, Lapidus, Alla, Clum, Alicia, 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

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

Author

Clum, Alicia, 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, Lapidus, Alla, Clum, Alicia, 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

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

5. The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

Author

Challacombe, Jean F., 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, Brettin, Thomas S., Challacombe, Jean F., 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.

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

6. The Complete Genome Sequence of Bacillus thuringiensis Al Hakam

Author

Challacombe, Jean F., 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, Brettin, Thomas S., Challacombe, Jean F., 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.

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

7. The US DOE Joint Genome Institute Microbial Genome Program

Author

Lapidus, Alla, 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, Richardson, Paul M., Lapidus, Alla, 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.

Published
2005

8. Automation of Fosmid Preps at the Joint Genome Institute

Author

Pollard, Martin, Pollard, Martin, Wilson, Steven, Gray, Bruce, Roberts, Simon, Alessi, Joseph, Yang, Dou-Shuan, Jett, Jamie, Mihalkanin, Danielle, Naca, Christine, Glavina, Tijana, Pollard, Martin, Pollard, Martin, Wilson, Steven, Gray, Bruce, Roberts, Simon, Alessi, Joseph, Yang, Dou-Shuan, Jett, Jamie, Mihalkanin, Danielle, Naca, Christine, and Glavina, Tijana

Published
2005

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

Author

Lucas, Susan M., 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, Rubin, Eddy, Lucas, Susan M., 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

Published
2005

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

Author

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

11. Developing custom picking software using the Genetix SDK

Author

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

Published
2005

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

Author

Han, Cliff S., 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, Brettin, Thomas S., Han, Cliff S., 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.

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

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

Author

Han, Cliff S., 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, Brettin, Thomas S., Han, Cliff S., 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.

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

14. The US DOE Joint Genome Institute Microbial Genome Program

Author

Lapidus, Alla, 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, Richardson, Paul M., Lapidus, Alla, 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.

Published
2005

15. Automation of Fosmid Preps at the Joint Genome Institute

Author

Pollard, Martin, Pollard, Martin, Wilson, Steven, Gray, Bruce, Roberts, Simon, Alessi, Joseph, Yang, Dou-Shuan, Jett, Jamie, Mihalkanin, Danielle, Naca, Christine, Glavina, Tijana, Pollard, Martin, Pollard, Martin, Wilson, Steven, Gray, Bruce, Roberts, Simon, Alessi, Joseph, Yang, Dou-Shuan, Jett, Jamie, Mihalkanin, Danielle, Naca, Christine, and Glavina, Tijana

Published
2005

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

Author

Lucas, Susan M., 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, Rubin, Eddy, Lucas, Susan M., 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

Published
2005

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

Author

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

18. Developing custom picking software using the Genetix SDK

Author

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

Published
2005

19. 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

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

Author

Martin, Joel, 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., Ustaszewska, Anna, Martin, Joel, 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

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

21. The complete sequence of human chromosome 5

Author

Schmutz, Jeremy, 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., Rubin, Edward M., Schmutz, Jeremy, 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.

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

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

Author

Martin, Joel, 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., Ustaszewska, Anna, Martin, Joel, 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

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

23. The complete sequence of human chromosome 5

Author

Schmutz, Jeremy, 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., Rubin, Edward M., Schmutz, Jeremy, 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.

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

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