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1.
Genome Announc ; 2(1)2014 Jan 23.
Article in English | MEDLINE | ID: mdl-24459263

ABSTRACT

We report the draft genome sequence of Mortierella alpina isolate CDC-B6842. M. alpina is a nonpathogenic member of the Mucoromycotina subphylum of fungi that is an important model for understanding the molecular mechanisms of lipid production and metabolism.

2.
Nat Commun ; 4: 2091, 2013.
Article in English | MEDLINE | ID: mdl-23820484

ABSTRACT

DNA cytosine methylation is a widely conserved epigenetic mark in eukaryotes that appears to have critical roles in the regulation of genome structure and transcription. Genome-wide methylation maps have so far only been established from the supergroups Archaeplastida and Unikont. Here we report the first whole-genome methylome from a stramenopile, the marine model diatom Phaeodactylum tricornutum. Around 6% of the genome is intermittently methylated in a mosaic pattern. We find extensive methylation in transposable elements. We also detect methylation in over 320 genes. Extensive gene methylation correlates strongly with transcriptional silencing and differential expression under specific conditions. By contrast, we find that genes with partial methylation tend to be constitutively expressed. These patterns contrast with those found previously in other eukaryotes. By going beyond plants, animals and fungi, this stramenopile methylome adds significantly to our understanding of the evolution of DNA methylation in eukaryotes.


Subject(s)
DNA Methylation/genetics , Diatoms/genetics , Genome/genetics , Chromosomes/genetics , DNA Transposable Elements/genetics , Gene Expression Profiling , Gene Expression Regulation , Genetic Loci/genetics , Repetitive Sequences, Nucleic Acid/genetics
3.
J Bacteriol ; 194(11): 3026-7, 2012 Jun.
Article in English | MEDLINE | ID: mdl-22582382

ABSTRACT

We report the draft genome sequences of the collection referred to as the Escherichia coli DECA collection, which was assembled to contain representative isolates of the 15 most common diarrheagenic clones in humans (http://shigatox.net/new/). These genomes represent a valuable resource to the community of researchers who examine these enteric pathogens.


Subject(s)
Diarrhea/microbiology , Escherichia coli Infections/microbiology , Escherichia coli/genetics , Genome, Bacterial , Base Sequence , Child, Preschool , Escherichia coli/classification , Escherichia coli/isolation & purification , Female , Humans , Infant , Male , Molecular Sequence Data
4.
PLoS Pathog ; 4(2): e1000012, 2008 Feb 29.
Article in English | MEDLINE | ID: mdl-18463694

ABSTRACT

The H1N1 subtype of influenza A virus has caused substantial morbidity and mortality in humans, first documented in the global pandemic of 1918 and continuing to the present day. Despite this disease burden, the evolutionary history of the A/H1N1 virus is not well understood, particularly whether there is a virological basis for several notable epidemics of unusual severity in the 1940s and 1950s. Using a data set of 71 representative complete genome sequences sampled between 1918 and 2006, we show that segmental reassortment has played an important role in the genomic evolution of A/H1N1 since 1918. Specifically, we demonstrate that an A/H1N1 isolate from the 1947 epidemic acquired novel PB2 and HA genes through intra-subtype reassortment, which may explain the abrupt antigenic evolution of this virus. Similarly, the 1951 influenza epidemic may also have been associated with reassortant A/H1N1 viruses. Intra-subtype reassortment therefore appears to be a more important process in the evolution and epidemiology of H1N1 influenza A virus than previously realized.


Subject(s)
Disease Outbreaks , Evolution, Molecular , Genes, Viral , Genome, Viral , Influenza A Virus, H1N1 Subtype/genetics , Reassortant Viruses/genetics , Hemagglutinins, Viral , Humans , Influenza A Virus, H1N1 Subtype/isolation & purification , Influenza, Human/virology , Phylogeny , RNA, Viral/chemistry , RNA, Viral/genetics , RNA-Dependent RNA Polymerase/genetics , Recombination, Genetic , Viral Proteins/genetics
5.
Emerg Infect Dis ; 13(5): 713-8, 2007 May.
Article in English | MEDLINE | ID: mdl-17553249

ABSTRACT

To better understand the ecology and epidemiology of the highly pathogenic avian influenza virus in its transcontinental spread, we sequenced and analyzed the complete genomes of 36 recent influenza A (H5N1) viruses collected from birds in Europe, northern Africa, and southeastern Asia. These sequences, among the first complete genomes of influenza (H5N1) viruses outside Asia, clearly depict the lineages now infecting wild and domestic birds in Europe and Africa and show the relationships among these isolates and other strains affecting both birds and humans. The isolates fall into 3 distinct lineages, 1 of which contains all known non-Asian isolates. This new Euro-African lineage, which was the cause of several recent (2006) fatal human infections in Egypt and Iraq, has been introduced at least 3 times into the European-African region and has split into 3 distinct, independently evolving sublineages. One isolate provides evidence that 2 of these sublineages have recently reassorted.


Subject(s)
Birds/virology , Evolution, Molecular , Genes, Viral/genetics , Influenza A Virus, H5N1 Subtype/genetics , Influenza in Birds/genetics , Africa, Northern/epidemiology , Animals , Europe/epidemiology , Influenza A Virus, H5N1 Subtype/classification , Influenza in Birds/classification , Middle East/epidemiology , Molecular Epidemiology , Molecular Sequence Data , Phylogeny
6.
PLoS Pathog ; 2(12): e125, 2006 Dec.
Article in English | MEDLINE | ID: mdl-17140286

ABSTRACT

Understanding the evolutionary dynamics of influenza A virus is central to its surveillance and control. While immune-driven antigenic drift is a key determinant of viral evolution across epidemic seasons, the evolutionary processes shaping influenza virus diversity within seasons are less clear. Here we show with a phylogenetic analysis of 413 complete genomes of human H3N2 influenza A viruses collected between 1997 and 2005 from New York State, United States, that genetic diversity is both abundant and largely generated through the seasonal importation of multiple divergent clades of the same subtype. These clades cocirculated within New York State, allowing frequent reassortment and generating genome-wide diversity. However, relatively low levels of positive selection and genetic diversity were observed at amino acid sites considered important in antigenic drift. These results indicate that adaptive evolution occurs only sporadically in influenza A virus; rather, the stochastic processes of viral migration and clade reassortment play a vital role in shaping short-term evolutionary dynamics. Thus, predicting future patterns of influenza virus evolution for vaccine strain selection is inherently complex and requires intensive surveillance, whole-genome sequencing, and phenotypic analysis.


Subject(s)
Evolution, Molecular , Genes, Viral , Influenza A Virus, H3N2 Subtype/genetics , Influenza, Human/virology , Antigenic Variation , Antigens, Viral/genetics , Gene Flow , Genetic Variation , Genome , Humans , Influenza A Virus, H3N2 Subtype/immunology , Influenza, Human/immunology , New York , Phylogeny , Population Surveillance , Stochastic Processes
7.
Nature ; 437(7062): 1162-6, 2005 Oct 20.
Article in English | MEDLINE | ID: mdl-16208317

ABSTRACT

Influenza viruses are remarkably adept at surviving in the human population over a long timescale. The human influenza A virus continues to thrive even among populations with widespread access to vaccines, and continues to be a major cause of morbidity and mortality. The virus mutates from year to year, making the existing vaccines ineffective on a regular basis, and requiring that new strains be chosen for a new vaccine. Less-frequent major changes, known as antigenic shift, create new strains against which the human population has little protective immunity, thereby causing worldwide pandemics. The most recent pandemics include the 1918 'Spanish' flu, one of the most deadly outbreaks in recorded history, which killed 30-50 million people worldwide, the 1957 'Asian' flu, and the 1968 'Hong Kong' flu. Motivated by the need for a better understanding of influenza evolution, we have developed flexible protocols that make it possible to apply large-scale sequencing techniques to the highly variable influenza genome. Here we report the results of sequencing 209 complete genomes of the human influenza A virus, encompassing a total of 2,821,103 nucleotides. In addition to increasing markedly the number of publicly available, complete influenza virus genomes, we have discovered several anomalies in these first 209 genomes that demonstrate the dynamic nature of influenza transmission and evolution. This new, large-scale sequencing effort promises to provide a more comprehensive picture of the evolution of influenza viruses and of their pattern of transmission through human and animal populations. All data from this project are being deposited, without delay, in public archives.


Subject(s)
Evolution, Molecular , Genome, Viral , Influenza A virus/genetics , Influenza, Human/virology , Mutagenesis/genetics , Animals , Hemagglutinin Glycoproteins, Influenza Virus/genetics , Hemagglutinin Glycoproteins, Influenza Virus/immunology , History, 20th Century , History, 21st Century , Humans , Influenza A virus/classification , Influenza A virus/isolation & purification , Influenza A virus/physiology , Influenza Vaccines/history , Influenza Vaccines/immunology , Influenza, Human/epidemiology , Influenza, Human/transmission , Influenza, Human/veterinary , Mutation/genetics , Neuraminidase/genetics , Neuraminidase/metabolism , New York/epidemiology , Phylogeny , Public Sector , Reassortant Viruses/genetics , Sequence Analysis , Time Factors , Virus Replication
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