15 research outputs found
Genome Analysis Linking Recent European and African Influenza (H5N1) Viruses
Although linked, these viruses are distinct from earlier outbreak strains
Metabolic Complementarity and Genomics of the Dual Bacterial Symbiosis of Sharpshooters
Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter (Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192–base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects (e.g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission
The Evolutionary Genetics and Emergence of Avian Influenza Viruses in Wild Birds
We surveyed the genetic diversity among avian influenza virus (AIV) in wild birds, comprising 167 complete viral genomes from 14 bird species sampled in four locations across the United States. These isolates represented 29 type A influenza virus hemagglutinin (HA) and neuraminidase (NA) subtype combinations, with up to 26% of isolates showing evidence of mixed subtype infection. Through a phylogenetic analysis of the largest data set of AIV genomes compiled to date, we were able to document a remarkably high rate of genome reassortment, with no clear pattern of gene segment association and occasional inter-hemisphere gene segment migration and reassortment. From this, we propose that AIV in wild birds forms transient “genome constellations,” continually reshuffled by reassortment, in contrast to the spread of a limited number of stable genome constellations that characterizes the evolution of mammalian-adapted influenza A viruses
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Metabolic complementarity and genomics of the dual bacterial symbiosis of sharpshooters
Mutualistic intracellular symbiosis between bacteria and insects is a widespread phenomenon that has contributed to the global success of insects. The symbionts, by provisioning nutrients lacking from diets, allow various insects to occupy or dominate ecological niches that might otherwise be unavailable. One such insect is the glassy-winged sharpshooter ( Homalodisca coagulata), which feeds on xylem fluid, a diet exceptionally poor in organic nutrients. Phylogenetic studies based on rRNA have shown two types of bacterial symbionts to be coevolving with sharpshooters: the gamma-proteobacterium Baumannia cicadellinicola and the Bacteroidetes species Sulcia muelleri. We report here the sequencing and analysis of the 686,192-base pair genome of B. cicadellinicola and approximately 150 kilobase pairs of the small genome of S. muelleri, both isolated from H. coagulata. Our study, which to our knowledge is the first genomic analysis of an obligate symbiosis involving multiple partners, suggests striking complementarity in the biosynthetic capabilities of the two symbionts: B. cicadellinicola devotes a substantial portion of its genome to the biosynthesis of vitamins and cofactors required by animals and lacks most amino acid biosynthetic pathways, whereas S. muelleri apparently produces most or all of the essential amino acids needed by its host. This finding, along with other results of our genome analysis, suggests the existence of metabolic codependency among the two unrelated endosymbionts and their insect host. This dual symbiosis provides a model case for studying correlated genome evolution and genome reduction involving multiple organisms in an intimate, obligate mutualistic relationship. In addition, our analysis provides insight for the first time into the differences in symbionts between insects ( e. g., aphids) that feed on phloem versus those like H. coagulata that feed on xylem. Finally, the genomes of these two symbionts provide potential targets for controlling plant pathogens such as Xylella fastidiosa, a major agroeconomic problem, for which H. coagulata and other sharpshooters serve as vectors of transmission
Predicted Metabolic Pathways in <i>Baumannia</i> and the Predicted Amino Acid Biosynthesis Pathways Encoded by the Partial Genome Sequence of <i>Sulcia</i>
<p>Genes that are present are in red and the corresponding catalytic pathways are illustrated in solid black lines; the genes that are absent in the
<i>Baumannia</i> genome and genes that have not been identified in the partial
<i>Sulcia</i> genome are in gray, and the corresponding metabolic steps are illustrated in gray lines.
</p
Maximum-Likelihood Tree of <i>Sulcia</i> with Species in the <i>Bacteroides and Chlorobi</i> Phyla for which Complete Genomes Are Available
<p>The tree was build using the PHYML program from the concatenated alignments of 34 ribosomal proteins. The bootstrap values are based upon 1,000 replications.</p
Genome-Based Phylogenetic Analysis of <i>Baumannia</i>
<div><p>(A) Maximum-likelihood tree of gamma-proteobacterial endosymbionts. The tree was built from concatenated alignments of 45 ribosomal proteins using the PHYML program. The bootstrap value is based upon 1,000 replications.</p>
<p>(B) Gene order comparison of
<i>Baumannia</i> and
Blochmannia floridanus. The plot shows the locations of homologous proteins between the two genomes.
</p></div
Circular View of the <i>Baumannia</i> Genome
<p>Circles correspond to the following features, starting with the outermost circle: (1) forward strand genes, (2) reverse strand genes, (3) χ<sup>2</sup> deviation of local nucleotide composition from the genome average, (4) GC skew, (5) tRNAs (green lines), (6) rRNAs (blue lines); and (7) small RNAs (red lines). Color legend for CDSs and number of genes in each category are at the bottom.
</p
The Distribution into Functional Role Categories of the 166 Predicted Genes Encoded in the 146,384-bp Partial Sequence of the <i>Sulcia</i> Genome
<p>Data are shown for all ORFs that encode proteins longer than 45 amino acids that have BLASTP matches with an E-value less than 10<sup>−3</sup> to proteins in complete genomes. Different fragments of the same gene are counted as one gene in the chart.
</p