10 research outputs found
Characteristics of contigs with homology to viral protein sequences in the libraries.
<p>Characteristics of contigs with homology to viral protein sequences in the libraries.</p
Hits of nuclear genes against KEGG BRITE Ontology database using the KAAS pipeline for the 16 genomic libraries.
<p>The number of hits is listed below the species name. Colours assigned according to the highest level of KEGG Orthology hierarchy (different organismal/cellular pathway groups/ecosystem processes).</p
Correlation between genomic library size (y-axis) and total length of mitochondrial genome recovered (x-axis).
<p>A significantly positive linear correlation (Pearson r = 0.6049, P = 0.0219) between the number of base pairs sequenced and the proportion of the mitochondrial genome recovered was found.</p
Bacterial hits found in four genomic libraries.
<p>Hits for the bacterial species are displayed next to the chart pie for species with ≥4% of the hits. For the three pycnogonid species, Gammaproteobacteria are predominant, whereas for the vent limpet <i>Lepetodrilus</i> sp. nov. different bacterial groups were detected. The colours of the charts relate to the phyla/classes of Bacteria (see legend).</p
Characteristics of contigs with homology to known transposable elements in the libraries.
<p>Characteristics of contigs with homology to known transposable elements in the libraries.</p
rRNA genes found in the different libraries.
<p>The total number of reads, the number of assembled contigs with coverage and the total unique rRNA gene bp are listed.</p
Coverage estimations for the sequenced genomic libraries based upon genome size information of closely related taxa found in the Animal Genome Size database.
*<p>Information on genome size of <i>Euphausia superba</i> is based upon the flow-cytometry estimates listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Jeffery1" target="_blank">[46]</a>.</p
Total number and genomic density of microsatellites found in the libraries before and after applying stringent filtering criteria (best primers, single read contigs only, see Supporting information S3 for further information).
<p>Results are given for three different sets of search parameters which correspond to search parameters in: Mayer et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Mayer2" target="_blank">[48]</a> but filtering for perfect microsatellites only, Santana et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Santana1" target="_blank">[15]</a>, Gardner et al. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Gardner1" target="_blank">[4]</a>.</p
Percentage of contigs with candidate microsatellites found in the non-enriched libraries with three different search parameter settings.
<p>Search parameter settings were adapted from the three studies <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Gardner1" target="_blank">[4]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Santana1" target="_blank">[15]</a>, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Mayer2" target="_blank">[48]</a> and used in Phobos <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0049202#pone.0049202-Mayer1" target="_blank">[47]</a> runs. Numbers on top of the columns represent the total number of perfect microsatellites retained after restrictive filtering for quality criteria.</p
Workflow showing the methodological approach followed in this study.
<p>In this study we used a MySQL database (*) for storing the contigs. Other database formats are possible or reads can also be stored locally without a specific database.</p