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35 results on '"Zafar, Nikhat"'

1. Genome Analysis of Multiple Pathogenic Isolates of Streptococcus agalactiae: Implications for the Microbial "Pan-Genome"

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., Angiuoli, Samuel V., Crabtree, Jonathan, Jones, Amanda L., Durkin, A. Scott, DeBoy, Robert T., Davidsen, Tanja M., Mora, Marirosa, Scarselli, Maria, Peterson, Jeremy D., Hauser, Christopher R., Sundaram, Jaideep P., Nelson, William C., Madupu, Ramana, Brinkac, Lauren M., Dodson, Robert J., Rosovitz, Mary J., Sullivan, Steven A., Daugherty, Sean C., Haft, Daniel H., Selengut, Jeremy, Gwinn, Michelle L., Zhou, Liwei, Zafar, Nikhat, Khouri, Hoda, Radune, Diana, Dimitrov, George, Watkins, Kisha, Smith, Shannon, Utterback, Teresa R., White, Owen, Rubens, Craig E., Grandi, Guido, Madoff, Lawrence C., Kasper, Dennis L., Telford, John L., Wessels, Michael R., Rappuoli, Rino, and Fraser, Claire M.

Published
2005

2. Structural Flexibility in the Burkholderia mallei Genome

Author

Nierman, William C., DeShazer, David, Kim, H. Stanley, Tettelin, Herve, Nelson, Karen E., Feldblyum, Tamara, Ulrich, Ricky L., Ronning, Catherine M., Brinkac, Lauren M., Daugherty, Sean C., Davidsen, Tanja D., Deboy, Robert T., Dimitrov, George, Dodson, Robert J., Durkin, A. Scott, Gwinn, Michelle L., Haft, Daniel H., Khouri, Hoda, Kolonay, James F., Madupu, Ramana, Mohammoud, Yasmin, Nelson, William C., Radune, Diana, Romero, Claudia M., Sarria, Saul, Selengut, Jeremy, Shamblin, Christine, Sullivan, Steven A., White, Owen, Yu, Yan, Zafar, Nikhat, Zhou, Liwei, Fraser, Claire M., and Greenberg, E. Peter

Published
2004

3. The Complete Genome Sequence of the Arabidopsis and Tomato Pathogen Pseudomonas syringae pv. tomato DC3000

Author

Buell, C. Robin, Joardar, Vinita, Lindeberg, Magdalen, Selengut, Jeremy, Paulsen, Ian T., Gwinn, Michelle L., Dodson, Robert J., Deboy, Robert T., Durkin, A. Scott, Kolonay, James F., Madupu, Ramana, Daugherty, Sean, Brinkac, Lauren, Beanan, Maureen J., Haft, Daniel H., Nelson, William C., Davidsen, Tanja, Zafar, Nikhat, Zhou, Liwei, Liu, Jia, Yuan, Qiaoping, Khouri, Hoda, Fedorova, Nadia, Tran, Bao, Russell, Daniel, Berry, Kristi, Utterback, Teresa, Van Aken, Susan E., Feldblyum, Tamara V., D'Ascenzo, Mark, Deng, Wen-Ling, Ramos, Adela R., Alfano, James R., Cartinhour, Samuel, Chatterjee, Arun K., Delaney, Terrence P., Lazarowitz, Sondra G., Martin, Gregory B., Schneider, David J., Tang, Xiaoyan, Bender, Carol L., White, Owen, Fraser, Claire M., and Collmer, Alan

Published
2003

4. Comparative Genomics of Emerging Human Ehrlichiosis Agents

Author

Hotopp, Julie C Dunning, Lin, Mingqun, Madupu, Ramana, Crabtree, Jonathan, Angiuoli, Samuel V, Eisen, Jonathan, Seshadri, Rekha, Ren, Qinghu, Wu, Martin, Utterback, Teresa R, Smith, Shannon, Lewis, Matthew, Khouri, Hoda, Zhang, Chunbin, Niu, Hua, Lin, Quan, Ohashi, Norio, Zhi, Ning, Nelson, William, Brinkac, Lauren M, Dodson, Robert J, Rosovitz, MJ, Sundaram, Jaideep, Daugherty, Sean C, Davidsen, Tanja, Durkin, Anthony S, Gwinn, Michelle, Haft, Daniel H, Selengut, Jeremy D, Sullivan, Steven A, Zafar, Nikhat, Zhou, Liwei, Benahmed, Faiza, Forberger, Heather, Halpin, Rebecca, Mulligan, Stephanie, Robinson, Jeffrey, White, Owen, Rikihisa, Yasuko, and Tettelin, Hervé

Subjects
Infectious Diseases, Rare Diseases, Genetics, Biotechnology, Vector-Borne Diseases, Prevention, Emerging Infectious Diseases, Infection, Good Health and Well Being, Animals, Biotin, DNA Repair, Ehrlichia, Ehrlichiosis, Genome, Genomics, Humans, Models, Biological, Phylogeny, Rickettsia, Ticks, Developmental Biology
Abstract

Anaplasma (formerly Ehrlichia) phagocytophilum, Ehrlichia chaffeensis, and Neorickettsia (formerly Ehrlichia) sennetsu are intracellular vector-borne pathogens that cause human ehrlichiosis, an emerging infectious disease. We present the complete genome sequences of these organisms along with comparisons to other organisms in the Rickettsiales order. Ehrlichia spp. and Anaplasma spp. display a unique large expansion of immunodominant outer membrane proteins facilitating antigenic variation. All Rickettsiales have a diminished ability to synthesize amino acids compared to their closest free-living relatives. Unlike members of the Rickettsiaceae family, these pathogenic Anaplasmataceae are capable of making all major vitamins, cofactors, and nucleotides, which could confer a beneficial role in the invertebrate vector or the vertebrate host. Further analysis identified proteins potentially involved in vacuole confinement of the Anaplasmataceae, a life cycle involving a hematophagous vector, vertebrate pathogenesis, human pathogenesis, and lack of transovarial transmission. These discoveries provide significant insights into the biology of these obligate intracellular pathogens. © 2006 Dunning Hotopp.

Published
2006

6. Comparative genomic evidence for a close relationship between the dimorphic prosthecate bacteria Hyphomonas neptunium and Caulobacter crescentus

Author

Badger, Jonathan H., Hoover, Timothy R., Brun, Yves V., Weiner, Ronald M., Laub, Michael T., Alexandre, Gladys, Mrazek, Jan, Ren, Qinghu, Paulsen, Ian T., Nelson, Karen E., Khouri, Hoda M., Radune, Diana, Sosa, Julia, Dodson, Robert J., Sullivan, Steven A., Rosovitz, M.J., Madupu, Ramana, Brinkac, Lauren M., Durkin, A. Scott, Daugherty, Sean C., Kothari, Sagar P., Giglio, Michelle Gwinn, Zhou, Liwei, Haft, Daniel H., Selengut, Jeremy D., Davidsen, Tanja M., Yang, Qi, Zafar, Nikhat, and Ward, Naomi L.

Subjects
Caulobacter -- Genetic aspects, Chemotaxis -- Research, Biological sciences
Abstract

The dimorphic prosthecate bacteria (DPB) are [alpha]-proteobacteria that reproduce in an asymmetric manner rather than by binary fission and are of interest as simple models of development. Prior to this work, the only member of this group for which genome sequence was available was the model freshwater organism Caulobacter crescentus. Here we describe the genome sequence of Hyphomonas neptunium, a marine member of the DPB that differs from C. crescentus in that H. neptunium uses its stalk as a reproductive structure. Genome analysis indicates that this organism shares more genes with C. crescentus than it does with Silicibacter pomeroyi (a closer relative according to 16S rRNA phylogeny), that it relies upon a heterotrophic strategy utilizing a wide range of substrates, that its cell cycle is likely to be regulated in a similar manner to that of C. crescentus, and that the outer membrane complements of H. neptunium and C. crescentus are remarkably similar. H. neptunium swarmer cells are highly motile via a single polar flagellum. With the exception of cheY and cheR, genes required for chemotaxis were absent in the H. neptunium genome. Consistent with this observation, H. neptunium swarmer cells did not respond to any chemotactic stimuli that were tested, which suggests that H. neptunium motility is a random dispersal mechanism for swarmer cells rather than a stimulus-controlled navigation system for locating specific environments. In addition to providing insights into bacterial development, the H. neptunium genome will provide an important resource for the study of other interesting biological processes including chromosome segregation, polar growth, and cell aging.

Published
2006

7. Whole-genome sequence analysis of Pseudomonas syringae pv. phaseolicola 1448A reveals divergence among pathovars in genes involved in virulence and transposition

Author

Joardar, Vinita, Lindeberg, Magdalen, Jackson, Robert W., Selengut, Jeremy, Dodson, Robert, Brinkac, Lauren M., Daugherty, Sean C., DeBoy, Robert, Durkin, A. Scott, Giglio, Michelle Gwinn, Madupu, Ramana, Nelson, William C., Rosovitz, M.J., Sullivan, Steven, Crabtree, Jonathan, Creasy, Todd, Davidsen, Tanja, Haft, Dan H., Zafar, Nikhat, Zhou, Liwei, Halpin, Rebecca, Holley, Tara, Khouri, Hoda, Feldblyum, Tamara, White, Owen, Fraser, Claire M., Chatterjee, Arun K., Cartinhour, Sam, Schneider, David J., Mansfield, John, Collmer, Alan, and Buell, C. Robin

Subjects
Genomics -- Comparative analysis, Genetic research -- Comparative analysis, Biological sciences
Abstract

Pseudomonas syringae pv. phaseolicola, a gram-negative bacterial plant pathogen, is the causal agent of halo blight of bean. In this study, we report on the genome sequence of P. syringae pv. phaseolicola isolate 1448A, which encodes 5,353 open reading frames (ORFs) on one circular chromosome (5,928,787 bp) and two plasmids (131,950 bp and 51,711 bp). Comparative analyses with a phylogenetically divergent pathovar, P. syringae pv. tomato DC3000, revealed a strong degree of conservation at the gene and genome levels. In total, 4,133 ORFs were identified as putative orthologs in these two pathovars using a reciprocal best-hit method, with 3,941 ORFs present in conserved, syntenic blocks. Although these two pathovars are highly similar at the physiological level, they have distinct host ranges; 1448A causes disease in beans, and DC3000 is pathogenic on tomato and Arabidopsis. Examination of the complement of ORFs encoding virulence, fitness, and survival factors revealed a substantial, but not complete, overlap between these two pathovars. Another distinguishing feature between the two pathovars is their distinctive sets of transposable elements. With access to a fifth complete pseudomonad genome sequence, we were able to identify 3,567 ORFs that likely comprise the core Pseudomonas genome and 365 ORFs that are P. syringae specific.

Published
2005

8. Pathema: a clade-specific bioinformatics resource center for pathogen research

Author

Brinkac, Lauren M., Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Caler, Elisabet, Dodson, Robert J., Durkin, A. Scott, Harkins, Derek M., Lorenzi, Hernan, Madupu, Ramana, Sebastian, Yinong, Shrivastava, Susmita, Thiagarajan, Mathangi, Orvis, Joshua, Sundaram, Jaideep P., Crabtree, Jonathon, Galens, Kevin, Zhao, Yongmei, Inman, Jason M., Montgomery, Robert, Schobel, Seth, Galinsky, Kevin, Tanenbaum, David M., Resnick, Adam, Zafar, Nikhat, White, Owen, and Sutton, Granger

Published
2010
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9. The comprehensive microbial resource

Author

Davidsen, Tanja, Beck, Erin, Ganapathy, Anuradha, Montgomery, Robert, Zafar, Nikhat, Yang, Qi, Madupu, Ramana, Goetz, Phil, Galinsky, Kevin, White, Owen, and Sutton, Granger

Published
2010
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11. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

Author

Joardar Vinita, Abrams Natalie F, Hostetler Jessica, Paukstelis Paul J, Pakala Suchitra, Pakala Suman B, Zafar Nikhat, Abolude Olukemi O, Payne Gary, Andrianopoulos Alex, Denning David W, and Nierman William C

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Results Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. Conclusions The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies. Despite the conservation of the core genes, the mitochondrial genomes of Aspergillus and Penicillium species examined here exhibit significant amount of interspecies variation. Most of this variation can be attributed to accessory genes and mobile introns, presumably acquired by horizontal gene transfer of mitochondrial plasmids and intron homing.

Published
2012
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12. Hidden genomic evolution in a morphospecies—The landscape of rapidly evolving genes in Tetrahymena

Author

Xiong, Jie, primary, Yang, Wentao, additional, Chen, Kai, additional, Jiang, Chuanqi, additional, Ma, Yang, additional, Chai, Xiaocui, additional, Yan, Guanxiong, additional, Wang, Guangying, additional, Yuan, Dongxia, additional, Liu, Yifan, additional, Bidwell, Shelby L., additional, Zafar, Nikhat, additional, Hadjithomas, Michalis, additional, Krishnakumar, Vivek, additional, Coyne, Robert S., additional, Orias, Eduardo, additional, and Miao, Wei, additional

Published
2019
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16. Corrections: Genome Analysis of Multiple Pathogenic Isolates of Streptococcus Agalactiae: Implications for the Microbial 'Pan-Genome'

Author

Tettelin, Hervé, Masignani, Vega, Cieslewicz, Michael J., Donati, Claudio, Medini, Duccio, Ward, Naomi L., Angiuoli, Samuel V., Crabtree, Jonathan, Jones, Amanda L., Durkin, A. Scott, DeBoy, Robert T., Davidsen, Tanja M., Mora, Marirosa, Scarselli, Maria, Peterson, Jeremy D., Hauser, Christopher R., Sundaram, Jaideep P., Nelson, William C., Madupu, Ramana, Brinkac, Lauren M., Dodson, Robert J., Rosovitz, Mary J., Sullivan, Steven A., Daugherty, Sean C., Haft, Daniel H., Selengut, Jeremy, Gwinn, Michelle L., Zhou, Liwei, Zafar, Nikhat, Khouri, Hoda, Radune, Diana, Dimitrov, George, Watkins, Kisha, Smith, Shannon, Utterback, Teresa R., White, Owen, Rubens, Craig E., Grandi, Guido, Madoff, Lawrence C., Kasper, Dennis L., Telford, John L., Wessels, Michael R., Rappuoli, Rino, and Fraser, Claire M.

Published
2005

17. Three genomes from the phylum Acidobacteria provide insight into the lifestyles of these microorganisms in soils

Author

Ward, Naomi L., Challacombe, Jean F., Janssen, Peter H., Henrissat, Bernard, Coutinho, Pedro M., Martin Wu, Xie, Gary, Haft, Daniel H., Sait, Michelle, Badger, Jonathan, Barabote, Ravi D., Bradley, Brent, Brettin, Thomas S., Brinkac, Lauren M., Bruce, David, Creasy, Todd, Daugherty, Sean C., Davidsen, Tanja M., DeBoy, Robert T., Detter, J. Chris, Dodson, Robert J., Durkin, A. Scott, Ganapathy, Anuradha, Gwinn-Giglio, Michelle, Han, Cliff S., Khouri, Hoda, Kiss, Hajnalka, Kothari, Sagar P., Madupu, Ramana, Nelson, Karen E., Nelson, William C., Paulsen, Ian, Penn, Kevin, Qinghu Ren, Rosovitz, M.J., Selengut, Jeremy D., Shrivastava, Susmita, Sullivan, Steven A., Tapia, Roxanne, Thompson, L. Sue, Watkins, Kisha L., Qi Yang, Chunhui Yu, Zafar, Nikhat, Zhou, Liwei, and Kuske, Cherly R.

Subjects
Bacterial genetics -- Research, Cyanobacteria -- Physiological aspects, Cyanobacteria -- Genetic aspects, Hydration (Chemistry) -- Analysis, Soil microbiology -- Research, Biological sciences
Abstract

The result from the comparison of complete genomes of three strains from the phylum Acidobacteria which share genomic traits with members of the Proteobacteria, the Cyanobacteria, and the Fungi are presented. The cells of the isolates of Acidobacteria strains are found to be long-lived, divide slowly, exhibit slow metabolic rates under low-nutrient conditions and are well equipped to tolerate fluctuations in soil hydration.

Published
2009

18. Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Author

Hamilton, Eileen P, primary, Kapusta, Aurélie, additional, Huvos, Piroska E, additional, Bidwell, Shelby L, additional, Zafar, Nikhat, additional, Tang, Haibao, additional, Hadjithomas, Michalis, additional, Krishnakumar, Vivek, additional, Badger, Jonathan H, additional, Caler, Elisabet V, additional, Russ, Carsten, additional, Zeng, Qiandong, additional, Fan, Lin, additional, Levin, Joshua Z, additional, Shea, Terrance, additional, Young, Sarah K, additional, Hegarty, Ryan, additional, Daza, Riza, additional, Gujja, Sharvari, additional, Wortman, Jennifer R, additional, Birren, Bruce W, additional, Nusbaum, Chad, additional, Thomas, Jainy, additional, Carey, Clayton M, additional, Pritham, Ellen J, additional, Feschotte, Cédric, additional, Noto, Tomoko, additional, Mochizuki, Kazufumi, additional, Papazyan, Romeo, additional, Taverna, Sean D, additional, Dear, Paul H, additional, Cassidy-Hanley, Donna M, additional, Xiong, Jie, additional, Miao, Wei, additional, Orias, Eduardo, additional, and Coyne, Robert S, additional

Published
2016
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19. Author response: Structure of the germline genome of Tetrahymena thermophila and relationship to the massively rearranged somatic genome

Author

Hamilton, Eileen P, primary, Kapusta, Aurélie, additional, Huvos, Piroska E, additional, Bidwell, Shelby L, additional, Zafar, Nikhat, additional, Tang, Haibao, additional, Hadjithomas, Michalis, additional, Krishnakumar, Vivek, additional, Badger, Jonathan H, additional, Caler, Elisabet V, additional, Russ, Carsten, additional, Zeng, Qiandong, additional, Fan, Lin, additional, Levin, Joshua Z, additional, Shea, Terrance, additional, Young, Sarah K, additional, Hegarty, Ryan, additional, Daza, Riza, additional, Gujja, Sharvari, additional, Wortman, Jennifer R, additional, Birren, Bruce W, additional, Nusbaum, Chad, additional, Thomas, Jainy, additional, Carey, Clayton M, additional, Pritham, Ellen J, additional, Feschotte, Cédric, additional, Noto, Tomoko, additional, Mochizuki, Kazufumi, additional, Papazyan, Romeo, additional, Taverna, Sean D, additional, Dear, Paul H, additional, Cassidy-Hanley, Donna M, additional, Xiong, Jie, additional, Miao, Wei, additional, Orias, Eduardo, additional, and Coyne, Robert S, additional

Published
2016
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20. Draft Genome Sequence of the Plant-Pathogenic Soil Fungus Rhizoctonia solani Anastomosis Group 3 Strain Rhs1AP

Author

Cubeta, Marc A., primary, Thomas, Elizabeth, additional, Dean, Ralph A., additional, Jabaji, Suha, additional, Neate, Stephen M., additional, Tavantzis, Stellos, additional, Toda, Takeshi, additional, Vilgalys, Rytas, additional, Bharathan, Narayanaswamy, additional, Fedorova-Abrams, Natalie, additional, Pakala, Suman B., additional, Pakala, Suchitra M., additional, Zafar, Nikhat, additional, Joardar, Vinita, additional, Losada, Liliana, additional, and Nierman, William C., additional

Published
2014
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22. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Author

Clarke, Michael, Lohan, Amanda, Liu, Bernard, Lagkouvardos, Ilias, Roy, Scott, Zafar, Nikhat, Bertelli, Claire, Schilde, Christina, Kianianmomeni, Arash, Burglin, Thomas R., Frech, Christian, Turcotte, Bernard, Kopec, Klaus O., Synnott, John M., Choo, Caleb, Paponov, Ivan, Finkler, Aliza, Soon Heng Tan, Chris, Hutchins, Andrew P., Weinmeier, Thomas, Ratteri, Thomas, Chu, Jeffery SC, Gimenez, Gregory, Irimia, Manuel, Rigden, Daniel J., Fitzpatrick, David A., Lorenzo-Morales, Jacob, Baterman, Alex, Chiu, Cheng-Hsun, Tang, Petrus, Hegemann, Peter, Fromm, Hillel, Raoult, Didier, Greub, Gilbert, Miranda-Saavedra, Diego, Chen, Nansheng, Nash, Piers, Ginger, Michael L., Horn, Matthias, Schaap, Pauline, Caler, Lis, Loftus, Brendan J., Clarke, Michael, Lohan, Amanda, Liu, Bernard, Lagkouvardos, Ilias, Roy, Scott, Zafar, Nikhat, Bertelli, Claire, Schilde, Christina, Kianianmomeni, Arash, Burglin, Thomas R., Frech, Christian, Turcotte, Bernard, Kopec, Klaus O., Synnott, John M., Choo, Caleb, Paponov, Ivan, Finkler, Aliza, Soon Heng Tan, Chris, Hutchins, Andrew P., Weinmeier, Thomas, Ratteri, Thomas, Chu, Jeffery SC, Gimenez, Gregory, Irimia, Manuel, Rigden, Daniel J., Fitzpatrick, David A., Lorenzo-Morales, Jacob, Baterman, Alex, Chiu, Cheng-Hsun, Tang, Petrus, Hegemann, Peter, Fromm, Hillel, Raoult, Didier, Greub, Gilbert, Miranda-Saavedra, Diego, Chen, Nansheng, Nash, Piers, Ginger, Michael L., Horn, Matthias, Schaap, Pauline, Caler, Lis, and Loftus, Brendan J.

Abstract

Background The Amoebozoa constitute one of the primary divisio ns of eukaryotes encompassing taxa of both biomedic al and evolutionary importance, yet its genomic divers ity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii ( Ac ) the first representative from a solitary free-living amoebozoan. Results Ac encodes 15,455 compact intron rich genes a signifi cant number of which are predicted to have arisen through interkingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communicati on repertoire including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An impor tant environmental host of a diverse range of bacte ria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors many with predicted orthologous functions in the innate immune systems of higher organisms. Conclusions Our analysis highlights the important role of LGT i n the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall the availabil ity of an Ac genome should aid in deciphering the biology of th e Amoebozoa and facilitate functional genomic studi es in this important model organism and environmental host.

Published
2013

23. Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

Author

Joardar, Vinita, Joardar, Vinita, Abrams, Natalie F, Hostetler, Jessica, Paukstelis, Paul J, Pakala, Suchitra, Pakala, Suman B, Zafar, Nikhat, Abolude, Olukemi O, Payne, Gary, Andrianopoulos, Alex, Denning, David W, Nierman, William C, Joardar, Vinita, Joardar, Vinita, Abrams, Natalie F, Hostetler, Jessica, Paukstelis, Paul J, Pakala, Suchitra, Pakala, Suman B, Zafar, Nikhat, Abolude, Olukemi O, Payne, Gary, Andrianopoulos, Alex, Denning, David W, and Nierman, William C

Abstract

The genera Aspergillus and Penicillium include some of the most beneficial as well as the most harmful fungal species such as the penicillin-producer Penicillium chrysogenum and the human pathogen Aspergillus fumigatus, respectively. Their mitochondrial genomic sequences may hold vital clues into the mechanisms of their evolution, population genetics, and biology, yet only a handful of these genomes have been fully sequenced and annotated. Here we report the complete sequence and annotation of the mitochondrial genomes of six Aspergillus and three Penicillium species: A. fumigatus, A. clavatus, A. oryzae, A. flavus, Neosartorya fischeri (A. fischerianus), A. terreus, P. chrysogenum, P. marneffei, and Talaromyces stipitatus (P. stipitatum). The accompanying comparative analysis of these and related publicly available mitochondrial genomes reveals wide variation in size (25–36 Kb) among these closely related fungi. The sources of genome expansion include group I introns and accessory genes encoding putative homing endonucleases, DNA and RNA polymerases (presumed to be of plasmid origin) and hypothetical proteins. The two smallest sequenced genomes (A. terreus and P. chrysogenum) do not contain introns in protein-coding genes, whereas the largest genome (T. stipitatus), contains a total of eleven introns. All of the sequenced genomes have a group I intron in the large ribosomal subunit RNA gene, suggesting that this intron is fixed in these species. Subsequent analysis of several A. fumigatus strains showed low intraspecies variation. This study also includes a phylogenetic analysis based on 14 concatenated core mitochondrial proteins. The phylogenetic tree has a different topology from published multilocus trees, highlighting the challenges still facing the Aspergillus systematics. The study expands the genomic resources available to fungal biologists by providing mitochondrial genomes with consistent annotations for future genetic, evolutionary and population studies

Published
2012

24. Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogenRhizoctonia solaniAG-3

Author

Losada, Liliana, primary, Pakala, Suman B., additional, Fedorova, Natalie D., additional, Joardar, Vinita, additional, Shabalina, Svetlana A., additional, Hostetler, Jessica, additional, Pakala, Suchitra M., additional, Zafar, Nikhat, additional, Thomas, Elizabeth, additional, Rodriguez-Carres, Marianela, additional, Dean, Ralph, additional, Vilgalys, Rytas, additional, Nierman, William C., additional, and Cubeta, Marc A., additional

Published
2014
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25. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Author

Clarke, Michael, primary, Lohan, Amanda J, additional, Liu, Bernard, additional, Lagkouvardos, Ilias, additional, Roy, Scott, additional, Zafar, Nikhat, additional, Bertelli, Claire, additional, Schilde, Christina, additional, Kianianmomeni, Arash, additional, Bürglin, Thomas R, additional, Frech, Christian, additional, Turcotte, Bernard, additional, Kopec, Klaus O, additional, Synnott, John M, additional, Choo, Caleb, additional, Paponov, Ivan, additional, Finkler, Aliza, additional, Heng Tan, Chris, additional, Hutchins, Andrew P, additional, Weinmeier, Thomas, additional, Rattei, Thomas, additional, Chu, Jeffery SC, additional, Gimenez, Gregory, additional, Irimia, Manuel, additional, Rigden, Daniel J, additional, Fitzpatrick, David A, additional, Lorenzo-Morales, Jacob, additional, Bateman, Alex, additional, Chiu, Cheng-Hsun, additional, Tang, Petrus, additional, Hegemann, Peter, additional, Fromm, Hillel, additional, Raoult, Didier, additional, Greub, Gilbert, additional, Miranda-Saavedra, Diego, additional, Chen, Nansheng, additional, Nash, Piers, additional, Ginger, Michael L, additional, Horn, Matthias, additional, Schaap, Pauline, additional, Caler, Lis, additional, and Loftus, Brendan J, additional

Published
2013
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26. The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data

Author

Tanenbaum, David M., primary, Goll, Johannes, additional, Murphy, Sean, additional, Kumar, Prateek, additional, Zafar, Nikhat, additional, Thiagarajan, Mathangi, additional, Madupu, Ramana, additional, Davidsen, Tanja, additional, Kagan, Leonid, additional, Kravitz, Saul, additional, Rusch, Douglas B., additional, and Yooseph, Shibu, additional

Published
2010
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27. The comprehensive microbial resource

Author

Davidsen, Tanja, primary, Beck, Erin, additional, Ganapathy, Anuradha, additional, Montgomery, Robert, additional, Zafar, Nikhat, additional, Yang, Qi, additional, Madupu, Ramana, additional, Goetz, Phil, additional, Galinsky, Kevin, additional, White, Owen, additional, and Sutton, Granger, additional

Published
2009
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28. Pathema: a clade-specific bioinformatics resource center for pathogen research

Author

Brinkac, Lauren M., primary, Davidsen, Tanja, additional, Beck, Erin, additional, Ganapathy, Anuradha, additional, Caler, Elisabet, additional, Dodson, Robert J., additional, Durkin, A. Scott, additional, Harkins, Derek M., additional, Lorenzi, Hernan, additional, Madupu, Ramana, additional, Sebastian, Yinong, additional, Shrivastava, Susmita, additional, Thiagarajan, Mathangi, additional, Orvis, Joshua, additional, Sundaram, Jaideep P., additional, Crabtree, Jonathon, additional, Galens, Kevin, additional, Zhao, Yongmei, additional, Inman, Jason M., additional, Montgomery, Robert, additional, Schobel, Seth, additional, Galinsky, Kevin, additional, Tanenbaum, David M., additional, Resnick, Adam, additional, Zafar, Nikhat, additional, White, Owen, additional, and Sutton, Granger, additional

Published
2009
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29. Comparative Genomics of Emerging Human Ehrlichiosis Agents

Author

Dunning Hotopp, Julie C., primary, Lin, Mingqun, additional, Madupu, Ramana, additional, Crabtree, Jonathan, additional, Angiuoli, Samuel V, additional, Eisen, Jonathan, additional, Seshadri, Rekha, additional, Ren, Qinghu, additional, Wu, Martin, additional, Utterback, Teresa R, additional, Smith, Shannon, additional, Lewis, Matthew, additional, Khouri, Hoda, additional, Zhang, Chunbin, additional, Niu, Hua, additional, Lin, Quan, additional, Ohashi, Norio, additional, Zhi, Ning, additional, Nelson, William, additional, Brinkac, Lauren M, additional, Dodson, Robert J, additional, Rosovitz, M. J, additional, Sundaram, Jaideep, additional, Daugherty, Sean C, additional, Davidsen, Tanja, additional, Durkin, Anthony S, additional, Gwinn, Michelle, additional, Haft, Daniel H, additional, Selengut, Jeremy D, additional, Sullivan, Steven A, additional, Zafar, Nikhat, additional, Zhou, Liwei, additional, Benahmed, Faiza, additional, Forberger, Heather, additional, Halpin, Rebecca, additional, Mulligan, Stephanie, additional, Robinson, Jeffrey, additional, White, Owen, additional, Rikihisa, Yasuko, additional, and Tettelin, Hervé, additional

Published
2006
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30. Correction: Comparative Genomics of Emerging Human Ehrlichiosis Agents

Author

Dunning Hotopp, Julie C., primary, Lin, Mingqun, additional, Madupu, Ramana, additional, Crabtree, Jonathan, additional, Angiuoli, Samuel V., additional, Eisen, Jonathan A., additional, Seshadri, Rekha, additional, Ren, Qinghu, additional, Wu, Martin, additional, Utterback, Teresa R., additional, Smith, Shannon, additional, Lewis, Matthew, additional, Khouri, Hoda, additional, Zhang, Chunbin, additional, Niu, Hua, additional, Lin, Quan, additional, Ohashi, Norio, additional, Zhi, Ning, additional, Nelson, William, additional, Brinkac, Lauren M., additional, Dodson, Robert J., additional, Rosovitz, M. J., additional, Sundaram, Jaideep, additional, Daugherty, Sean C., additional, Davidsen, Tanja, additional, Durkin, Anthony S., additional, Gwinn, Michelle, additional, Haft, Daniel H., additional, Selengut, Jeremy D., additional, Sullivan, Steven A., additional, Zafar, Nikhat, additional, Zhou, Liwei, additional, Benahmed, Faiza, additional, Forberger, Heather, additional, Halpin, Rebecca, additional, Mulligan, Stephanie, additional, Robinson, Jeffrey, additional, White, Owen, additional, Rikihisa, Yasuko, additional, and Tettelin, Hervé, additional

Published
2006
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32. The genome sequence of the anaerobic, sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough

Author

Heidelberg, John F, primary, Seshadri, Rekha, additional, Haveman, Shelley A, additional, Hemme, Christopher L, additional, Paulsen, Ian T, additional, Kolonay, James F, additional, Eisen, Jonathan A, additional, Ward, Naomi, additional, Methe, Barbara, additional, Brinkac, Lauren M, additional, Daugherty, Sean C, additional, Deboy, Robert T, additional, Dodson, Robert J, additional, Durkin, A Scott, additional, Madupu, Ramana, additional, Nelson, William C, additional, Sullivan, Steven A, additional, Fouts, Derrick, additional, Haft, Daniel H, additional, Selengut, Jeremy, additional, Peterson, Jeremy D, additional, Davidsen, Tanja M, additional, Zafar, Nikhat, additional, Zhou, Liwei, additional, Radune, Diana, additional, Dimitrov, George, additional, Hance, Mark, additional, Tran, Kevin, additional, Khouri, Hoda, additional, Gill, John, additional, Utterback, Terry R, additional, Feldblyum, Tamara V, additional, Wall, Judy D, additional, Voordouw, Gerrit, additional, and Fraser, Claire M, additional

Published
2004
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33. Mobile elements and mitochondrial genome expansion in the soil fungus and potato pathogen Rhizoctonia solani AG-3.

Author

Losada, Liliana, Pakala, Suman B., Fedorova, Natalie D., Joardar, Vinita, Shabalina, Svetlana A., Hostetler, Jessica, Pakala, Suchitra M., Zafar, Nikhat, Thomas, Elizabeth, Rodriguez-Carres, Marianela, Dean, Ralph, Vilgalys, Rytas, Nierman, William C., and Cubeta, Marc A.

Subjects
MITOCHONDRIAL enzymes, MITOCHONDRIAL pathology, RHIZOCTONIA diseases, RHIZOCTONIA solani, PLANT genetic engineering, GENETIC transcription in plants, GENETICS
Abstract

The soil fungus Rhizoctonia solani is an economically important pathogen of agricultural and forestry crops. Here, we present the complete sequence and analysis of the mitochondrial genome of R. solani, field isolate Rhs1 AP. The genome (235 849 bp) is the largest mitochondrial genome of a filamentous fungus sequenced to date and exhibits a rich accumulation of introns, novel repeat sequences, homing endonuclease genes, and hypothetical genes. Stable secondary structures exhibited by repeat sequences suggest that they comprise functional, possibly catalytic RNA elements. RNA-Seq expression profiling confirmed that the majority of homing endonuclease genes and hypothetical genes are transcriptionally active. Comparative analysis suggests that the mitochondrial genome of R. solani is an example of a dynamic history of expansion in filamentous fungi. [ABSTRACT FROM AUTHOR]

Published
2014
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34. CoreGenes: A computational tool for identifying and cataloging 'core' genes in a set of small genomes

Author

Seto Donald, Mazumder Raja, and Zafar Nikhat

Subjects
Viral Structural Proteins, Internet, Chloroplasts, Genes, Essential, Genome, Genes, Viral, Software Validation, Computational Biology, Genome, Viral, Genomics, lcsh:Computer applications to medicine. Medical informatics, Methodology article, Genes, Plant, Mitochondria, lcsh:Biology (General), Genes, Software Design, Databases, Genetic, lcsh:R858-859.7, natural sciences, Programming Languages, lcsh:QH301-705.5, Algorithms, Genome, Plant, Software
Abstract

Background Improvements in DNA sequencing technology and methodology have led to the rapid expansion of databases comprising DNA sequence, gene and genome data. Lower operational costs and heightened interest resulting from initial intriguing novel discoveries from genomics are also contributing to the accumulation of these data sets. A major challenge is to analyze and to mine data from these databases, especially whole genomes. There is a need for computational tools that look globally at genomes for data mining. Results CoreGenes is a global JAVA-based interactive data mining tool that identifies and catalogs a "core" set of genes from two to five small whole genomes simultaneously. CoreGenes performs hierarchical and iterative BLASTP analyses using one genome as a reference and another as a query. Subsequent query genomes are compared against each newly generated "consensus." These iterations lead to a matrix comprising related genes from this set of genomes, e. g., viruses, mitochondria and chloroplasts. Currently the software is limited to small genomes on the order of 330 kilobases or less. Conclusion A computational tool CoreGenes has been developed to analyze small whole genomes globally. BLAST score-related and putatively essential "core" gene data are displayed as a table with links to GenBank for further data on the genes of interest. This web resource is available at http://pumpkins.ib3.gmu.edu:8080/CoreGenes or http://www.bif.atcc.org/CoreGenes.

Published
2002

35. Genome of Acanthamoeba castellaniihighlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling

Author

Clarke, Michael, Lohan, Amanda, Liu, Bernard, Lagkouvardos, Ilias, Roy, Scott, Zafar, Nikhat, Bertelli, Claire, Schilde, Christina, Kianianmomeni, Arash, Bürglin, Thomas, Frech, Christian, Turcotte, Bernard, Kopec, Klaus, Synnott, John, Choo, Caleb, Paponov, Ivan, Finkler, Aliza, Heng Tan, Chris, Hutchins, Andrew, Weinmeier, Thomas, Rattei, Thomas, Chu, Jeffery, Gimenez, Gregory, Irimia, Manuel, Rigden, Daniel, Fitzpatrick, David, Lorenzo-Morales, Jacob, Bateman, Alex, Chiu, Cheng-Hsun, Tang, Petrus, Hegemann, Peter, Fromm, Hillel, Raoult, Didier, Greub, Gilbert, Miranda-Saavedra, Diego, Chen, Nansheng, Nash, Piers, Ginger, Michael, Horn, Matthias, Schaap, Pauline, Caler, Lis, and Loftus, Brendan

Abstract

The Amoebozoa constitute one of the primary divisions of eukaryotes, encompassing taxa of both biomedical and evolutionary importance, yet its genomic diversity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii(Ac) the first representative from a solitary free-living amoebozoan. Acencodes 15,455 compact intron-rich genes, a significant number of which are predicted to have arisen through inter-kingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Acappears to have incorporated them into established transcriptional programs. Acmanifests a complex signaling and cell communication repertoire, including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An important environmental host of a diverse range of bacteria and viruses, Acutilizes a diverse repertoire of predicted pattern recognition receptors, many with predicted orthologous functions in the innate immune systems of higher organisms. Our analysis highlights the important role of LGT in the biology of Acand in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall, the availability of an Acgenome should aid in deciphering the biology of the Amoebozoa and facilitate functional genomic studies in this important model organism and environmental host.

Published
2013
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