Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens

<p>Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens</p

Box and blob plots.

<p>(A) Box plots reporting results for numbers of homologs detected for 65 highly conserved orthologs in 5 PPN species analyzed. Results for <i>G</i>. <i>ellingtonae</i> are not included because this species was found to encode a single homolog for all 65 orthologs. (B) and (C) Blob plot results for <i>X</i>. <i>americanum</i> and <i>P</i>. <i>penetrans</i>, respectively. Colors indicate BLAST matches to different species of bacteria.</p

Genome skimming summary information and effector gene hits.

<p>Genome skimming summary information and effector gene hits.</p

Genome skimming schematic.

<p>Boxes progressing diagonally from top left to bottom right show steps typical of conventional genome projects. Grey boxes show steps shared by genome skimming and conventional genome projects. Red boxes, arrows, and Xs show conventional genome project steps eliminated in the genome skimming approach. Green boxes show analyses specific to our genome skimming strategy.</p

Maximum likelihood bootstrap tree of aligned ITS-rDNA gene sequences for populations of <i>Xiphinema americanum</i>, presented in 4 parts (A–D).

<p>Trees generated from the analysis of 204 newly generated ITS sequences from <i>X. americanum</i> and 4 sequences previously available from GenBank (2 of <i>X. americanum</i>, 1 <i>X. citricolum</i> and 1 <i>X. peruvianum</i>). <i>X. peruvianum</i> GQ231531.1 was designated as an outgroup. Sequence names consist of a population designation (e.g. WA-1; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090035#pone-0090035-t001" target="_blank">Table 1</a>) followed by a number to indicate the individual and a letter to indicate the clone (e.g. WA-1.1b is clone “b” from individual 1 from population WA-1). From 2 to 6 clones were sequenced for each individual nematode from 12 populations. Bootstrap values for clades supported at greater than 50% are shown. Brackets and V+/− indicate the presence or absence of nematode transmitted plant virus in those populations, excluding GenBank taxa indicated with an * for which virus status is unknown.</p

Schematic of loci of mitochondrial DNA analyzed.

<p>Rectangles with solid colors show mtDNA protein-coding genes, dashed rectangles show ribosomal RNA genes, and white rectangles show tRNA genes (single-letter abbreviations for associated amino acids). The dashed lines on top indicate the regions amplified in the two long PCRs used to generate templates for Illumina sequencing. Information about regions used for phylogenetic analyses is provided at the bottom.</p

<i>Xiphinema americanum</i> species complex populations included in this study.

a<p>Presence of nepovirus was based upon ELISA detection, direct observation of symptoms, or historical data for the site.</p

Maximum likelihood bootstrap tree of aligned ∼1.1 kb of mtDNA for populations of <i>Xiphinema americanum</i>.

<p>Thirty-two nematode sequences were analyzed. Sequence names consist of a population designation (e.g. WA-1; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090035#pone-0090035-t001" target="_blank">Table 1</a>) followed by a number to indicate the individual (e.g. WA-1.1). Presence or absence of nematode transmitted plant virus in an individual nematode indicated by virus (+/−).</p

Maximum likelihood bootstrap tree of aligned ∼2.5 kb of mtDNA for populations of <i>Xiphinema americanum</i>.

<p>Thirteen nematode sequences were analyzed. Sequence names consist of a population designation (e.g. WA-1; see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090035#pone-0090035-t001" target="_blank">Table 1</a>) followed by a number to indicate the individual (e.g. WA-1.1). Presence or absence of nematode transmitted plant virus in an individual nematode indicated by virus (+/−).</p