Table 1.
Species analysed in this study and characteristics of the libraries.
Figure 1.
Workflow showing the methodological approach followed in this study.
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.
Table 2.
Coverage estimations for the sequenced genomic libraries based upon genome size information of closely related taxa found in the Animal Genome Size database.
Figure 2.
Percentage of contigs with candidate microsatellites found in the non-enriched libraries with three different search parameter settings.
Search parameter settings were adapted from the three studies [4], [15], [48] and used in Phobos [47] runs. Numbers on top of the columns represent the total number of perfect microsatellites retained after restrictive filtering for quality criteria.
Table 3.
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).
Figure 3.
Percentage of contigs with microsatellites or minisatellites found in the non-enriched genomic libraries.
Search parameters were according to Mayer et al. [48] used in Phobos [47]. For the analysis, repeats with a perfection greater or equal to 95% were retained. The numbers on top of the columns represent the total number found per library.
Figure 4.
Overview over the different mitochondrial genes found in the non-enriched libraries.
The upper section indicates full (dark blue) and partial (bright blue) mitochondrial protein-coding or rRNA genes recovered. The pie chart indicates the proportion and total number of tRNAs found. In the lower section the total contig lengths (in kb) of mitochondrial genes is shown.
Figure 5.
Correlation between genomic library size (y-axis) and total length of mitochondrial genome recovered (x-axis).
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.
Table 4.
Summary of the nuclear gene identification in the genomic and enriched libraries.
Figure 6.
Hits of nuclear genes against KEGG BRITE Ontology database using the KAAS pipeline for the 16 genomic libraries.
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).
Table 5.
rRNA genes found in the different libraries.
Table 6.
Characteristics of contigs with homology to known transposable elements in the libraries.
Figure 7.
Bacterial hits found in four genomic libraries.
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 Lepetodrilus sp. nov. different bacterial groups were detected. The colours of the charts relate to the phyla/classes of Bacteria (see legend).
Table 7.
Characteristics of contigs with homology to viral protein sequences in the libraries.