Journal Article10.1016/J.GDE.2005.09.006
The microbial pan-genome
1.2K
TL;DR: A decade after the beginning of the genomic era, the question of how genomics can describe a bacterial species has not been fully addressed and the pan-genome, which is composed of a "core genome" containing genes present in all strains, and a "dispensable genome", might be orders of magnitude larger than any single genome.
read more
About: This article is published in Current Opinion in Genetics & Development. The article was published on 01 Dec 2005. The article focuses on the topics: Minimal genome & Bacterial genome size.
read more
Chat with Paper
AI Agents for this Paper
Find similar papers on Google Scholar, PubMed and Arxiv
Write a critical review of this paper
Analyze citations of this paper to find unaddressed research gaps
Citations
Pangenomic analysis reveals pathogen-specific regions and novel effector candidates in Fusarium oxysporum f.sp. cepae
Andrew D. Armitage,Andrew Taylor,Maria K. Sobczyk,Laura Baxter,Bethany P. J. Greenfield,Helen J. Bates,Fiona M. Wilson,Alison C. Jackson,Sascha Ott,Richard J. Harrison,John P. Clarkson +10 more
TL;DR: RNA-seq expression studies identified candidate effectors expressed in planta, consisting of both known effector homologs and novel candidates, and found FTF1 and a subset of other transcription factors implicated in regulation of effector expression were found to be expressed in Planta.
Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism
Disa Bäckström,Natalya Yutin,Steffen Leth Jørgensen,Jennah Dharamshi,Felix Homa,Katarzyna Zaremba-Niedwiedzka,Anja Spang,Anja Spang,Yuri I. Wolf,Eugene V. Koonin,Thijs J. G. Ettema +10 more
TL;DR: The assembled new virus genomes substantially expand the known diveristy of the Nucleo-Cytoplasmic Large DNA Viruses of eukaryotes, and support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.
5
Reference-agnostic representation and visualization of pan-genomes.
Qihua Liang,Stefano Lonardi +1 more
TL;DR: PGV as mentioned in this paper is a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering, which enables an intuitive, effective and interactive visualization of a pangenome.
Genomics of Xanthomonas citri and Related Species
Neha Jalan,Qing Yan,Sunitha Kogenaru,Yinping Guo,Jeffrey B. Jones,James H. Graham,Nian Wang +6 more
- 01 Jan 2014
TL;DR: Multilocus sequence phylogenetic analysis of XCCA and other xanthomonads indicates that citrus canker pathogens XccA, XccAw, XauB, and XauC form a closely related group.
5
SVCollector: Optimized sample selection for cost-efficient long-read population sequencing
T. Rhyker Ranallo-Benavidez,Zachary H. Lemmon,Sebastian Soyk,Sergey Aganezov,William J Salerno,Rajiv C. McCoy,Zachary B. Lippman,Zachary B. Lippman,Michael C. Schatz,Michael C. Schatz,Fritz J. Sedlazeck +10 more
TL;DR: The number of variants present in cohorts of different sizes selected using SVCollector follows a power-law distribution that is naturally related to the population genetic concept of the allele frequency spectrum, allowing us to estimate the diversity present with increasing numbers of samples.
References
Diversity of the human intestinal microbial flora.
Paul B. Eckburg,Elisabeth M. Bik,Charles N. Bernstein,Elizabeth Purdom,Les Dethlefsen,Michael Sargent,Steven R. Gill,Karen E. Nelson,David A. Relman,David A. Relman,David A. Relman +10 more
TL;DR: A majority of the bacterial sequences corresponded to uncultivated species and novel microorganisms, and significant intersubject variability and differences between stool and mucosa community composition were discovered.
Environmental Genome Shotgun Sequencing of the Sargasso Sea
J. Craig Venter,Karin A. Remington,John F. Heidelberg,Aaron L. Halpern,Doug Rusch,Jonathan A. Eisen,Dongying Wu,Ian T. Paulsen,Karen E. Nelson,William C. Nelson,Derrick E. Fouts,Samuel Levy,Anthony H. Knap,Michael W. Lomas,Kenneth H. Nealson,Owen White,Jeremy Peterson,Jeff Hoffman,Rachel Parsons,Holly Baden-Tillson,Cynthia Pfannkoch,Yu-Hui Rogers,Hamilton O. Smith +22 more
TL;DR: Over 1.2 million previously unknown genes represented in these samples, including more than 782 new rhodopsin-like photoreceptors are identified, suggesting substantial oceanic microbial diversity.
Genome analysis of multiple pathogenic isolates of Streptococcus agalactiae: Implications for the microbial “pan-genome”
Hervé Tettelin,Vega Masignani,Michael J. Cieslewicz,Claudio Donati,Duccio Medini,Naomi L. Ward,Samuel V. Angiuoli,Jonathan Crabtree,Amanda L. Jones,A. Scott Durkin,Robert T. DeBoy,Tanja M. Davidsen,Marirosa Mora,Maria Scarselli,Immaculada Margarit Y Ros,Jeremy Peterson,Christopher R. Hauser,Jaideep P. Sundaram,William C. Nelson,Ramana Madupu,Lauren M. Brinkac,Robert J. Dodson,M. J. Rosovitz,Steven A. Sullivan,Sean C. Daugherty,Daniel H. Haft,Jeremy D. Selengut,Michelle L. Gwinn,Liwei Zhou,Nikhat Zafar,Hoda Khouri,Diana Radune,George Dimitrov,Kisha Watkins,Kevin J. B. O'Connor,Shannon Smith,Teresa Utterback,Owen White,Craig E. Rubens,Guido Grandi,Lawrence C. Madoff,Dennis L. Kasper,John L. Telford,Michael R. Wessels,Rino Rappuoli,Claire M. Fraser +45 more
TL;DR: The genomic sequence of six strains representing the five major disease-causing serotypes of Streptococcus agalactiae, the main cause of neonatal infection in humans, was generated and Mathematical extrapolation of the data suggests that the gene reservoir available for inclusion in the S. agalactic pan-genome is vast and that unique genes will continue to be identified even after sequencing hundreds of genomes.
2.5K
Mobile elements: drivers of genome evolution.
TL;DR: Mobile elements within genomes have driven genome evolution in diverse ways and are becoming useful tools for learning more about genome evolution and gene function.
1.9K
Phages and the Evolution of Bacterial Pathogens: from Genomic Rearrangements to Lysogenic Conversion
TL;DR: The current review presents the available genomics and biological data on prophages from bacterial pathogens in an evolutionary framework to demonstrate that the chromosomes from bacteria and their viruses (bacteriophages) are coevolving.
1.7K