Supplementary Data for Hynes et al. (2016)

This data set contains sequences, sequence alignments and phylogenetic trees used in the bioinformatic analyses presented in:<br><pre>Hynes AP, Shakya M, Mercer RG, Grüll MP, Bown L, Davidson F, Steffen E, Matchem H, Peach ME, Berger T, Grebe K, Zhaxybayeva O, Lang AS. <i>Functional and Evolutionary Characterization of a Gene Transfer Agent's Multilocus "Genome".</i> Mol Biol Evol. <b>2016</b> Oct;<b>33(10)</b>:2530-43. Epub 2016 Jun 24.<br><br>doi: 10.1093/molbev/msw125. PubMed PMID: 27343288; <br>PubMed Central PMCID: PMC5026251.<br><br>The contents of four files:<br><br>1) <b>32core_genes.zip</b>: amino acid sequences of 32 gene families (in FASTA format) that were used to reconstruct Rhodobacterales phylogeny (shown in Figure 6 in the article.)<br>2) <b>rcc00171_tree.zip</b>: alignment (in FASTA format) and tree file (in NEWICK format) for the tree shown in Figure 7B.<br>3) <b>gtaNphage_teeNafa.zip</b>: alignments (in FASTA format) and tree files (in NEWICK format) for all RcGTA genes and their phage homologs (trees are shown in Figures 7A and S2.)<br>4) <b>RcGTA.zip</b>: amino acid sequences of genes in the RcGTA genome. These are also available in GenBank.<br></pre

Analysis of influenza A viruses from gulls: An evaluation of inter-regional movements and interactions with other avian and mammalian influenza A viruses

<p>Birds, including members of the families Anatidae (waterfowl) and Laridae (gulls and terns), serve as the major reservoir of influenza A viruses (IAVs). The ecogeographic contributions of gulls to global IAV dynamics, in terms of geographic scale and virus movements, are important and are distinct from those of waterfowl. Gulls primarily carry the H13 and H16 subtypes, yet can be infected by additional subtypes. Also, gulls are frequently infected by IAVs that contain mixtures of genes from different geographic phylogenetic lineages (e.g. North American and Eurasian). The present analysis examines a variety of viruses isolated from gulls and terns across the world that exhibit particularly high phylogenetic affinities to viruses found in other hosts. This illustrates the potential for gulls to act as highly pathogenic virus carriers, disseminators of viruses over long distances, and contributors in the genesis of pandemic strains. The historical evolution of an entirely Eurasian gull virus isolated in North America was also traced and indicates the Caspian Sea, in southwestern Asia, was an important area for the generation of this virus, and analysis of IAVs from terns also points to this region as relevant for the generation of novel strains.</p

Genome-wide identification and characterization of small RNAs in <i>Rhodobacter capsulatus</i> and identification of small RNAs affected by loss of the response regulator CtrA

<p>Small non-coding RNAs (sRNAs) are involved in the control of numerous cellular processes through various regulatory mechanisms, and in the past decade many studies have identified sRNAs in a multitude of bacterial species using RNA sequencing (RNA-seq). Here, we present the first genome-wide analysis of sRNA sequencing data in <i>Rhodobacter capsulatus</i>, a purple nonsulfur photosynthetic alphaproteobacterium. Using a recently developed bioinformatics approach, sRNA-Detect, we detected 422 putative sRNAs from <i>R. capsulatus</i> RNA-seq data. Based on their sequence similarity to sRNAs in a sRNA collection, consisting of published putative sRNAs from 23 additional bacterial species, and RNA databases, the sequences of 124 putative sRNAs were conserved in at least one other bacterial species; and, 19 putative sRNAs were assigned a predicted function. We bioinformatically characterized all putative sRNAs and applied machine learning approaches to calculate the probability of a nucleotide sequence to be a bona fide sRNA. The resulting quantitative model was able to correctly classify 95.2% of sequences in a validation set. We found that putative <i>cis-</i>targets for antisense and partially overlapping sRNAs were enriched with protein-coding genes involved in primary metabolic processes, photosynthesis, compound binding, and with genes forming part of macromolecular complexes. We performed differential expression analysis to compare the wild type strain to a mutant lacking the response regulator CtrA, an important regulator of gene expression in <i>R. capsulatus</i>, and identified 18 putative sRNAs with differing levels in the two strains. Finally, we validated the existence and expression patterns of four novel sRNAs by Northern blot analysis.</p

Spatial distribution of detections of the Atlantic flyway duck AIV sub-lineages in North American flyways.

<p>The box plots show the proportions of detections in each of the flyways for the gene sub-lineages that were identified in the 2006–2011 Atlantic flyway duck AIVs. The solid line in the box is the median. The top and bottom of the box are the first and third quartiles, respectively. The upper and lower horizontal lines represent 1.5X the difference between the first and third quartiles and any values falling outside of those are plotted as points. The detailed results for the each segment are provided in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0086999#pone.0086999.s005" target="_blank">Figure S5</a>.</p

Summary of gene lineage and gene type diversity by segment for the 109 Atlantic flyway duck AIVs from 2006–2011.

a<p>Gene lineages, sub-lineages and types are defined as sharing ≥90%, ≥95% and ≥99% nucleotide identity, respectively.</p

Genetic structure of the gene lineages and sub-lineages of the Atlantic flyway duck AIVs.

<p>The numbers of genes in each detected sub-lineage for each of the segments of the 109 Atlantic flyway duck AIVs are shown in the pie charts. AIV genes with ≥95% nucleotide identity by pairwise distance analysis were assigned in a sub-lineage. For the HA genes, sub-lineages 7F-1, 7F-2, 11C-2, 12A-1, 13A-1 and 16D-1 were each detected once and are not labelled. Similarly for the NA genes, sub-lineages 2G-1, 3A-1, 3D-1, 8A-3, 9A-2 and 9A-3 were each detected once and are not labelled.</p

Perpetuation of Atlantic flyway duck AIV gene types across time.

<p>The proportions of gene types identified in the Atlantic flyway viruses that were detected for >5 and >10 years in North America are shown for each segment. There were significant differences among the proportions for the HA, M and NS segments relative to the other segments for >5 years (χ² = 53.1, df = 7, P<0.0001) and >10 years (χ² = 66.5, df = 7, P<0.0001). Statistically different proportions for the segments are indicated with different letters (a, b and c).</p

Inter-continental reassortants identified in the 109 Atlantic flyway duck AIVs.

a<p>Eurasian avian origin.</p>b<p>Eurasian gull origin.</p>c<p>North American gull origin.</p