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1. Library preparation methodology can influence genomic and functional predictions in human microbiome research

Author

Jones, MB, Highlander, SK, Anderson, EL, Li, W, Dayrit, M, Klitgord, N, Fabani, MM, Seguritan, V, Green, J, Pride, DT, Yooseph, S, Biggs, W, Nelson, KE, and Craig Venter, J

Subjects
MD Multidisciplinary
Abstract

Observations from human microbiome studies are often conflicting or inconclusive. Many factors likely contribute to these issues including small cohort sizes, sample collection, and handling and processing differences. The field of microbiome research is moving from 16S rDNA gene sequencing to a more comprehensive genomic and functional representation through whole-genome sequencing (WGS) of complete communities. Here we performed quantitative and qualitative analyses comparingWGS metagenomic data from human stool specimens using the Illumina Nextera XT and Illumina TruSeq DNA PCR-free kits, and the KAPA Biosystems Hyper Prep PCR and PCR-free systems. Significant differences in taxonomy are observed among the four different next-generation sequencing library preparations using a DNA mock community and a cell control of known concentration. We also revealed biases in error profiles, duplication rates, and loss of reads representing organisms that have a high %G+C content that can significantly impact results. As with all methods, the use of benchmarking controls has revealed critical differences among methods that impact sequencing results and later would impact study interpretation. We recommend that the community adopt PCR-free-based approaches to reduce PCR bias that affects calculations of abundance and to improve assemblies for accurate taxonomic assignment. Furthermore, the inclusion of a known-input cell spike-in control provides accurate quantitation of organisms in clinical samples.

Published
2015

3. Evolution of genes and genomes on the Drosophila phylogeny

Author

Clark, Andrew G., Eisen, Michael B., Smith, Douglas R., Bergman, Casey M., Oliver, Brian, Markow, Therese A., Kaufman, Thomas C., Kellis, Manolis, Gelbart, William, Iyer, Venky N., Pollard, Daniel A., Sackton, Timothy B., Larracuente, Amanda M., Singh, Nadia D., Abad, Jose P., Abt, Dawn N., Adryan, Boris, Aguade, Montserrat, Akashi, Hiroshi, Anderson, Wyatt W., Aquadro, Charles F., Ardell, David H., Arguello, Roman, Artieri, Carlo G., Barbash, Daniel A., Barker, Daniel, Barsanti, Paolo, Batterham, Phil, Batzoglou, Serafim, Begun, Dave, Bhutkar, Arjun, Blanco, Enrico, Bosak, Stephanie A., Bradley, Robert K., Brand, Adrianne D., Brent, Michael R., Brooks, Angela N., Brown, Randall H., Butlin, Roger K., Caggese, Corrado, Calvi, Brian R., Bernardo de Carvalho, A., Caspi, Anat, Castrezana, Sergio, Celniker, Susan E., Chang, Jean L., Chapple, Charles, Chatterji, Sourav, Chinwalla, Asif, Civetta, Alberto, Clifton, Sandra W., Comeron, Josep M., Costello, James C., Coyne, Jerry A., Daub, Jennifer, David, Robert G., Delcher, Arthur L., Delehaunty, Kim, Do, Chuong B., Ebling, Heather, Edwards, Kevin, Eickbush, Thomas, Evans, Jay D., Filipski, Alan, Findeiß, Sven, Freyhult, Eva, Fulton, Lucinda, Fulton, Robert, Garcia, Ana C. L., Gardiner, Anastasia, Garfield, David A., Garvin, Barry E., Gibson, Greg, Gilbert, Don, Gnerre, Sante, Godfrey, Jennifer, Good, Robert, Gotea, Valer, Gravely, Brenton, Greenberg, Anthony J., Griffiths-Jones, Sam, Gross, Samuel, Guigo, Roderic, Gustafson, Erik A., Haerty, Wilfried, Hahn, Matthew W., Halligan, Daniel L., Halpern, Aaron L., Halter, Gillian M., Han, Mira V., Heger, Andreas, Hillier, LaDeana, Hinrichs, Angie S., Holmes, Ian, Hoskins, Roger A., Hubisz, Melissa J., Hultmark, Dan, Huntley, Melanie A., Jaffe, David B., Jagadeeshan, Santosh, Jeck, William R., Johnson, Justin, Jones, Corbin D., Jordan, William C., Karpen, Gary H., Kataoka, Eiko, Keightley, Peter D., Kheradpour, Pouya, Kirkness, Ewen F., Koerich, Leonardo B., Kristiansen, Karsten, Kudrna, Dave, Kulathinal, Rob J., Kumar, Sudhir, Kwok, Roberta, Lander, Eric, Langley, Charles H., Lapoint, Richard, Lazzaro, Brian P., Lee, So-Jeong, Levesque, Lisa, Li, Ruiqiang, Lin, Chiao-Feng, Lin, Michael F., Lindblad-Toh, Kerstin, Llopart, Ana, Long, Manyuan, Low, Lloyd, Lozovsky, Elena, Lu, Jian, Luo, Meizhong, Machado, Carlos A., Makalowski, Wojciech, Marzo, Mar, Matsuda, Muneo, Matzkin, Luciano, McAllister, Bryant, McBride, Carolyn S., McKernan, Brendan, McKernan, Kevin, Mendez-Lago, Maria, Minx, Patrick, Mollenhauer, Michael U., Montooth, Kristi, Mount, Stephen M., Mu, Xu, Myers, Eugene, Negre, Barbara, Newfeld, Stuart, Nielsen, Rasmus, Noor, Mohamed A. F., O'Grady, Patrick, Pachter, Lior, Papaceit, Montserrat, Parisi, Matthew J., Parisi, Michael, Parts, Leopold, Pedersen, Jakob S., Pesole, Graziano, Phillippy, Adam M., Ponting, Chris P., Pop, Mihai, Porcelli, Damiano, Powell, Jeffrey R., Prohaska, Sonja, Pruitt, Kim, Puig, Marta, Quesneville, Hadi, Ravi Ram, Kristipati, Rand, David, Rasmussen, Matthew D., Reed, Laura K., Reenan, Robert, Reily, Amy, Remington, Karin A., Rieger, Tania T., Ritchie, Michael G., Robin, Charles, Rogers, Yu-Hui, Rohde, Claudia, Rozas, Julio, Rubenfield, Marc J., Ruiz, Alfredo, Russo, Susan, Salzberg, Steven L., Sanchez-Gracia, Alejandro, Saranga, David J., Sato, Hajime, Schaeffer, Stephen W., Schatz, Michael C., Schlenke, Todd, Schwartz, Russell, Segarra, Carmen, Singh, Rama S., Sirot, Laura, Sirota, Marina, Sisneros, Nicholas B., Smith, Chris D., Smith, Temple F., Spieth, John, Stage, Deborah E., Stark, Alexander, Stephan, Wolfgang, Strausberg, Robert L., Strempel, Sebastian, Sturgill, David, Sutton, Granger, Sutton, Granger G., Tao, Wei, Teichmann, Sarah, Tobari, Yoshiko N., Tomimura, Yoshihiko, Tsolas, Jason M., Valente, Vera L. S., Venter, Eli, Craig Venter, J., Vicario, Saverio, Vieira, Filipe G., Vilella, Albert J., Villasante, Alfredo, Walenz, Brian, Wang, Jun, Wasserman, Marvin, Watts, Thomas, Wilson, Derek, Wilson, Richard K., Wing, Rod A., Wolfner, Mariana F., Wong, Alex, Ka-Shu Wong, Gane, Wu, Chung-I, Wu, Gabriel, Yamamoto, Daisuke, Yang, Hsiao-Pei, Yang, Shiaw-Pyng, Yorke, James A., Yoshida, Kiyohito, Zdobnov, Evgeny, Zhang, Peili, Zhang, Yu, Zimin, Aleksey V., Baldwin, Jennifer, Abdouelleil, Amr, Abdulkadir, Jamal, Abebe, Adal, Abera, Brikti, Abreu, Justin, Christophe Acer, St, Aftuck, Lynne, Alexander, Allen, An, Peter, Anderson, Erica, Anderson, Scott, Arachi, Harindra, Azer, Marc, Bachantsang, Pasang, Barry, Andrew, Bayul, Tashi, Berlin, Aaron, Bessette, Daniel, Bloom, Toby, Blye, Jason, Boguslavskiy, Leonid, Bonnet, Claude, Boukhgalter, Boris, Bourzgui, Imane, Brown, Adam, Cahill, Patrick, Channer, Sheridon, Cheshatsang, Yama, Chuda, Lisa, Citroen, Mieke, Collymore, Alville, Cooke, Patrick, Costello, Maura, D'Aco, Katie, Daza, Riza, De Haan, Georgius, DeGray, Stuart, DeMaso, Christina, Dhargay, Norbu, Dooley, Kimberly, Dooley, Erin, Doricent, Missole, Dorje, Passang, Dorjee, Kunsang, Dupes, Alan, Elong, Richard, Falk, Jill, Farina, Abderrahim, Faro, Susan, Ferguson, Diallo, Fisher, Sheila, Foley, Chelsea D., Franke, Alicia, Friedrich, Dennis, Gadbois, Loryn, Gearin, Gary, Gearin, Christina R., Giannoukos, Georgia, Goode, Tina, Graham, Joseph, Grandbois, Edward, Grewal, Sharleen, Gyaltsen, Kunsang, Hafez, Nabil, Hagos, Birhane, Hall, Jennifer, Henson, Charlotte, Hollinger, Andrew, Honan, Tracey, Huard, Monika D., Hughes, Leanne, Hurhula, Brian, Erii Husby, M, Kamat, Asha, Kanga, Ben, Kashin, Seva, Khazanovich, Dmitry, Kisner, Peter, Lance, Krista, Lara, Marcia, Lee, William, Lennon, Niall, Letendre, Frances, LeVine, Rosie, Lipovsky, Alex, Liu, Xiaohong, Liu, Jinlei, Liu, Shangtao, Lokyitsang, Tashi, Lokyitsang, Yeshi, Lubonja, Rakela, Lui, Annie, MacDonald, Pen, Magnisalis, Vasilia, Maru, Kebede, Matthews, Charles, McCusker, William, McDonough, Susan, Mehta, Teena, Meldrim, James, Meneus, Louis, Mihai, Oana, Mihalev, Atanas, Mihova, Tanya, Mittelman, Rachel, Mlenga, Valentine, Montmayeur, Anna, Mulrain, Leonidas, Navidi, Adam, Naylor, Jerome, Negash, Tamrat, Nguyen, Thu, Nguyen, Nga, Nicol, Robert, Norbu, Choe, Norbu, Nyima, Novod, Nathaniel, O'Neill, Barry, Osman, Sahal, Markiewicz, Eva, Oyono, Otero L., Patti, Christopher, Phunkhang, Pema, Pierre, Fritz, Priest, Margaret, Raghuraman, Sujaa, Rege, Filip, Reyes, Rebecca, Rise, Cecil, Rogov, Peter, Ross, Keenan, Ryan, Elizabeth, Settipalli, Sampath, Shea, Terry, Sherpa, Ngawang, Shi, Lu, Shih, Diana, Sparrow, Todd, Spaulding, Jessica, Stalker, John, Stange-Thomann, Nicole, Stavropoulos, Sharon, Stone, Catherine, Strader, Christopher, Tesfaye, Senait, Thomson, Talene, Thoulutsang, Yama, Thoulutsang, Dawa, Topham, Kerri, Topping, Ira, Tsamla, Tsamla, Vassiliev, Helen, Vo, Andy, Wangchuk, Tsering, Wangdi, Tsering, Weiand, Michael, Wilkinson, Jane, Wilson, Adam, Yadav, Shailendra, Young, Geneva, Yu, Qing, Zembek, Lisa, Zhong, Danni, Zimmer, Andrew, Zwirko, Zac, Alvarez, Pablo, Brockman, Will, Butler, Jonathan, Chin, CheeWhye, Grabherr, Manfred, Kleber, Michael, Mauceli, Evan, and MacCallum, Iain

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

Author(s): Drosophila 12 Genomes Consortium; Project Leaders; Andrew G. Clark (corresponding author) [1]; Michael B. Eisen (corresponding author) [2, 3]; Douglas R. Smith (corresponding author) [4]; Casey M. Bergman (corresponding [...]

Published
2007
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4. Preface

Author

ADAMS, M.D., primary, FIELDS, C., additional, and CRAIG VENTER, J., additional

Published
1994
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6. Microbial metagenome of urinary tract infection

Author

Moustafa, Ahmed, primary, Singh, Harinder, additional, Li, Weizhong, additional, Moncera, Kelvin J., additional, Torralba, Manolito G., additional, Yu, Yanbao, additional, Manuel, Oriol, additional, Biggs, William, additional, Craig Venter, J., additional, Nelson, Karen E., additional, Pieper, Rembert, additional, and Telenti, Amalio, additional

Published
2017
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9. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities

Author

Dupont, Chris L, primary, McCrow, John P, additional, Valas, Ruben, additional, Moustafa, Ahmed, additional, Walworth, Nathan, additional, Goodenough, Ursula, additional, Roth, Robyn, additional, Hogle, Shane L, additional, Bai, Jing, additional, Johnson, Zackary I, additional, Mann, Elizabeth, additional, Palenik, Brian, additional, Barbeau, Katherine A, additional, Craig Venter, J, additional, and Allen, Andrew E, additional

Published
2014
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10. Rapidly produced SAM® vaccine against H7N9 influenza is immunogenic in mice

Author

Hekele, Armin, primary, Bertholet, Sylvie, additional, Archer, Jacob, additional, Gibson, Daniel G, additional, Palladino, Giuseppe, additional, Brito, Luis A, additional, Otten, Gillis R, additional, Brazzoli, Michela, additional, Buccato, Scilla, additional, Bonci, Alessandra, additional, Casini, Daniele, additional, Maione, Domenico, additional, Qi, Zhi-Qing, additional, Gill, John E, additional, Caiazza, Nicky C, additional, Urano, Jun, additional, Hubby, Bolyn, additional, Gao, George F, additional, Shu, Yuelong, additional, De Gregorio, Ennio, additional, Mandl, Christian W, additional, Mason, Peter W, additional, Settembre, Ethan C, additional, Ulmer, Jeffrey B, additional, Craig Venter, J, additional, Dormitzer, Philip R, additional, Rappuoli, Rino, additional, and Geall, Andrew J, additional

Published
2013
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11. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage

Author

Dupont, Chris L, primary, Rusch, Douglas B, additional, Yooseph, Shibu, additional, Lombardo, Mary-Jane, additional, Alexander Richter, R, additional, Valas, Ruben, additional, Novotny, Mark, additional, Yee-Greenbaum, Joyclyn, additional, Selengut, Jeremy D, additional, Haft, Dan H, additional, Halpern, Aaron L, additional, Lasken, Roger S, additional, Nealson, Kenneth, additional, Friedman, Robert, additional, and Craig Venter, J, additional

Published
2011
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12. Genomes and gene expression across light and productivity gradients in eastern subtropical Pacific microbial communities.

Author

Dupont, Chris L, McCrow, John P, Valas, Ruben, Moustafa, Ahmed, Walworth, Nathan, Goodenough, Ursula, Roth, Robyn, Hogle, Shane L, Bai, Jing, Johnson, Zackary I, Mann, Elizabeth, Palenik, Brian, Barbeau, Katherine A, Craig Venter, J, and Allen, Andrew E

Subjects
GENE expression, BIOGEOCHEMISTRY, CHLOROPHYLL, MICROBIOLOGY, BACTERIA classification, BACTERIOPLANKTON
Abstract

Transitions in community genomic features and biogeochemical processes were examined in surface and subsurface chlorophyll maximum (SCM) microbial communities across a trophic gradient from mesotrophic waters near San Diego, California to the oligotrophic Pacific. Transect end points contrasted in thermocline depth, rates of nitrogen and CO2 uptake, new production and SCM light intensity. Relative to surface waters, bacterial SCM communities displayed greater genetic diversity and enrichment in putative sulfur oxidizers, multiple actinomycetes, low-light-adapted Prochlorococcus and cell-associated viruses. Metagenomic coverage was not correlated with transcriptional activity for several key taxa within Bacteria. Low-light-adapted Prochlorococcus, Synechococcus, and low abundance gamma-proteobacteria enriched in the>3.0-μm size fraction contributed disproportionally to global transcription. The abundance of these groups also correlated with community functions, such as primary production or nitrate uptake. In contrast, many of the most abundant bacterioplankton, including SAR11, SAR86, SAR112 and high-light-adapted Prochlorococcus, exhibited low levels of transcriptional activity and were uncorrelated with rate processes. Eukaryotes such as Haptophytes and non-photosynthetic Aveolates were prevalent in surface samples while Mamielles and Pelagophytes dominated the SCM. Metatranscriptomes generated with ribosomal RNA-depleted mRNA (total mRNA) coupled to in vitro polyadenylation compared with polyA-enriched mRNA revealed a trade-off in detection eukaryotic organelle and eukaryotic nuclear origin transcripts, respectively. Gene expression profiles of SCM eukaryote populations, highly similar in sequence identity to the model pelagophyte Pelagomonas sp. CCMP1756, suggest that pelagophytes are responsible for a majority of nitrate assimilation within the SCM. [ABSTRACT FROM AUTHOR]

Published
2015
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14. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Themotoga maritima

Author

Nelson, Karen E., Clayton, Rebecca A., Gill, Steven R., Gwinn, Michelle L., Dodson, Robert J., Haft, Daniel H., Hickey, Erin K., Peterson, Jeremy D., Nelson, William, C., Ketchum, karen A., McDonald, Lisa, Utterback, Teresa R., Malek, Joel, A., Linher, Katja D., Garrett, Mina M., Stewart, Ashley M., Cotton, Matthew D., Pratt, Matthew S., Phillips, Cheryl A., Richardson, Delwood., Heidelberg, John, Sutton, Granger, G., Fleischmann, Robert D., Eisen, Jonathan A., White, Owen, Salsberg, Steven L., Smith, Hamilton O., Craig Venter, J., and Fraser, Claire M.

Subjects
Bacteria -- Research, Chromosome mapping -- Research, Genomes -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

Thermotoga maritima, is a non-spore-forming bacterium and is one of the deepest and mostly slowly evolving lineages in the Eubacteria. The 1,860,725-base-pair genome of T. maritima MSB8 has 1,877 predicted coding regions. Several pathways are involved in degradation of sugars and plant polysaccharides, and T. maritima has the highest number of genes most similar to archaeal genes. Lateral gene transfer is believed to have occurred between thermophilic Eubacteria and Archaea.

Published
1999

15. The Malaria Genome Sequencing Project

Author

Gardner, Malcolm J., primary, Tettelin, Hervé, additional, Carucci, Daniel J., additional, Cummings, Leda M., additional, Adams, Mark D., additional, Smith, Hamilton O., additional, Craig Venter, J., additional, and Hoffman, Stephen L., additional

Published
1998
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18. Genomic insights to SAR86, an abundant and uncultivated marine bacterial lineage.

Author

Dupont, Chris L, Rusch, Douglas B, Yooseph, Shibu, Lombardo, Mary-Jane, Alexander Richter, R, Valas, Ruben, Novotny, Mark, Yee-Greenbaum, Joyclyn, Selengut, Jeremy D, Haft, Dan H, Halpern, Aaron L, Lasken, Roger S, Nealson, Kenneth, Friedman, Robert, and Craig Venter, J

Subjects
MARINE bacteria, GENOMES, RIBOSOMAL RNA, PROTEORHODOPSIN, ADENOSINE triphosphate, BIOMOLECULES, GENOMICS
Abstract

Bacteria in the 16S rRNA clade SAR86 are among the most abundant uncultivated constituents of microbial assemblages in the surface ocean for which little genomic information is currently available. Bioinformatic techniques were used to assemble two nearly complete genomes from marine metagenomes and single-cell sequencing provided two more partial genomes. Recruitment of metagenomic data shows that these SAR86 genomes substantially increase our knowledge of non-photosynthetic bacteria in the surface ocean. Phylogenomic analyses establish SAR86 as a basal and divergent lineage of γ-proteobacteria, and the individual genomes display a temperature-dependent distribution. Modestly sized at 1.25-1.7 Mbp, the SAR86 genomes lack several pathways for amino-acid and vitamin synthesis as well as sulfate reduction, trends commonly observed in other abundant marine microbes. SAR86 appears to be an aerobic chemoheterotroph with the potential for proteorhodopsin-based ATP generation, though the apparent lack of a retinal biosynthesis pathway may require it to scavenge exogenously-derived pigments to utilize proteorhodopsin. The genomes contain an expanded capacity for the degradation of lipids and carbohydrates acquired using a wealth of tonB-dependent outer membrane receptors. Like the abundant planktonic marine bacterial clade SAR11, SAR86 exhibits metabolic streamlining, but also a distinct carbon compound specialization, possibly avoiding competition. [ABSTRACT FROM AUTHOR]

Published
2012
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23. Complete analysis of the presenilin 1 gene in early onset Alzheimer's disease

Author

Hutton, M., Busfield, F., Wragg, M., Crook, R., Perez-Tur, J., Clark, R. F., Prihar, G., Talbot, C., Phillips, H., Wright, K., Baker, M., Lendon, C., Duff, K., Martinez, A., Houlden, H., Nichols, A., Karran, E., Roberts, G., Roques, P., Rossor, M., Craig Venter, J., Adams, M. D., Cline, R. T., Phillips, C. A., Fuldner, R. A., Hardy, J., and Alison Goate

33. Complete genome sequence of Neisseria meningitidis serogroup B strain MC58

Author

William C. Nelson, Debbie S. Parksey, Michelle L. Gwinn, Jonathan A. Eisen, John F. Heidelberg, J. Craig Venter, Karen A. Ketchum, Robert D. Fleischmann, Vincenzo Scarlato, John Gill, Robert J. Dodson, Haiying Qin, Hervé Tettelin, Robert T. DeBoy, Brian Dougherty, E. Richard Moxon, Jessica Vamathevan, Henry Cittone, Steven L. Salzberg, Nigel J. Saunders, Karen E. Nelson, Anne Ciecko, Li Sun, Hamilton O. Smith, Guido Grandi, Jeremy Peterson, Tanya Mason, Emily B. Clark, Owen White, Derek W. Hood, Claire M. Fraser, Erin Hickey, Eric Blair, T. Utterback, Vega Masignani, Alex C. Jeffries, John F. Peden, Daniel H. Haft, Matthew D. Cotton, Hoda Khouri, Mariagrazia Pizza, Rino Rappuoli, Tettelin H., Saunders N.J., Heidelberg J., Jeffries A.C., Nelson K.E., Eisen J.A., Ketchum K.A., Hood D.W., Peden J.F., Dodson R.J., Nelson W.C., Gwinn M.L., DeBoy R., Peterson J.D., Hickey E.K., Haft D.H., Salzberg S.L., White O., Fleischmann R.D., Dougherty B.A., Mason T., Ciecko A., Parksey D.S., Blair E., Cittone H., Clark E.B., Cotton M.D., Utterback T.R., Khouri H., Qin H., Vamathevan J., Gill J., Scarlato V., Masignani V., Pizza M., Grandi G., Sun L., Smith H.O., Fraser C.M., Moxon E.R., Rappuoli R., and Craig Venter J.

Subjects
Sequence analysis, genome sequence, genetic islands, phase variation, Molecular Sequence Data, Virulence, Bacteremia, Meningitis, Meningococcal, Neisseria meningitidis, medicine.disease_cause, Genome, Microbiology, Evolution, Molecular, Open Reading Frames, Bacterial Proteins, Operon, medicine, Antigenic variation, Humans, Serotyping, Gene, Bacterial Capsules, Phylogeny, Recombination, Genetic, Genetics, Phase variation, Antigens, Bacterial, Multidisciplinary, biology, Sequence Analysis, DNA, biology.organism_classification, Antigenic Variation, Meningococcal Infections, Fimbriae, Bacterial, Mutation, Neisseria lactamica, DNA Transposable Elements, Transformation, Bacterial, Genome, Bacterial
Abstract

The 2,272,351–base pair genome ofNeisseria meningitidisstrain MC58 (serogroup B), a causative agent of meningitis and septicemia, contains 2158 predicted coding regions, 1158 (53.7%) of which were assigned a biological role. Three major islands of horizontal DNA transfer were identified; two of these contain genes encoding proteins involved in pathogenicity, and the third island contains coding sequences only for hypothetical proteins. Insights into the commensal and virulence behavior ofN. meningitidiscan be gleaned from the genome, in which sequences for structural proteins of the pilus are clustered and several coding regions unique to serogroup B capsular polysaccharide synthesis can be identified. Finally,N. meningitidiscontains more genes that undergo phase variation than any pathogen studied to date, a mechanism that controls their expression and contributes to the evasion of the host immune system.

Published
2016
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34. A shotgun optical map of the entire Plasmodium falciparum genome.

Author

Lai Z, Jing J, Aston C, Clarke V, Apodaca J, Dimalanta ET, Carucci DJ, Gardner MJ, Mishra B, Anantharaman TS, Paxia S, Hoffman SL, Craig Venter J, Huff EJ, and Schwartz DC

Subjects
Animals, Chromosomes genetics, Chromosomes, Artificial, Yeast genetics, Contig Mapping methods, Electrophoresis, Gel, Pulsed-Field, Expressed Sequence Tags, Genomic Library, Image Processing, Computer-Assisted, Karyotyping methods, Optics and Photonics, Reproducibility of Results, Restriction Mapping methods, Sensitivity and Specificity, Genome, Protozoan, Physical Chromosome Mapping methods, Plasmodium falciparum genetics
Abstract

The unicellular parasite Plasmodium falciparum is the cause of human malaria, resulting in 1.7-2.5 million deaths each year. To develop new means to treat or prevent malaria, the Malaria Genome Consortium was formed to sequence and annotate the entire 24.6-Mb genome. The plan, already underway, is to sequence libraries created from chromosomal DNA separated by pulsed-field gel electrophoresis (PFGE). The AT-rich genome of P. falciparum presents problems in terms of reliable library construction and the relative paucity of dense physical markers or extensive genetic resources. To deal with these problems, we reasoned that a high-resolution, ordered restriction map covering the entire genome could serve as a scaffold for the alignment and verification of sequence contigs developed by members of the consortium. Thus optical mapping was advanced to use simply extracted, unfractionated genomic DNA as its principal substrate. Ordered restriction maps (BamHI and NheI) derived from single molecules were assembled into 14 deep contigs corresponding to the molecular karyotype determined by PFGE (ref. 3).

Published
1999
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