In fact, O. petrowi appears to be rich in microsatellites,

in which a total of 335 units of perfect SSRs were identified with a minimal length of 8 nt AR-13324 (Table 1). These included mononucleotides (228 units), dinucleotides (30), trinucleotides (56), tetranucleotides (11) and 10 repeats with 5–8 nucleotides. At least 98 contigs contained two or more SSRs, and 31 contigs contained 3–6 SSRs (Table 1). Examples included QEW_123 with 5 for mono-, tri- or tetra-nucleotide SSRs; QEW_126 with 5 mono-, tetra- or octa-nucleotide SSRs, and QEW_203 with 6 di-, tri- or penta-nucleotide SSRs (see Additional file 2: Table S2 for a complete list of detected microsatellite sequences). We also looked at the distribution of microsatellites with repeat units of ≥2 nt, which revealed ~2 or ~1.5 times more microsatellite sequences are present in contigs with no hits in BLAST/InterProScan searches (19.0%) or with hits but unknown function (14.4%) than in the annotatable contigs (9.9%) (Table 2).

In summary, the eye worm genome contains a rich number of microsatellite sequences with the potential to be further validated as potential genetic markers. Table 1 Statistics on the lengths of repeat units and numbers of microsatellite sequences per contig in Oxyspirura petrowi identified by the genome sequence survey Length of repeat unit ifenprodil Counts No. microsatellites per contig Counts 1 228 1 86 2 30 2 67 3 56 3 17 4 11 4 7 5 2 5 6 6 6 6 1 8 2 ≥7 0 Total microsatellites this website 335 Average no. per contig 1.82 Table 2 Number of microsatellites (SSR) with unit length ≥2 by functional groups* Group No. contigs SSR (unit > =2) Percentage Annotatable 121 12 9.9% Function unknown 90 13 14.4% No hits 137 26 19.0% Total 348 51 14.7% * See

Additional file 2: Table S2 for a complete list of microsatellite sequences. Phylogenetic position of O. petrowi based on 18S rRNA genes Our first phylogenetic analyses based on a large 18S rRNA dataset with BI and ML methods produced trees that agreed with those produced by others. While O. petrowi was clustered within the Spirurida clade, it was close to a branch consisting of Tetrameres fissipina and an unknown Onchoceridae species. This was likely a result caused by a long branch attraction (LBA) artifact based on the unusual long branch formed by T. fissipina and the Onchoceridae species, as well as by the obvious high numbers of nucleotide substitutions in these two sequences (data not shown). We also observed potential sequencing mistakes for the long 18S rRNA sequence of Thelazia lacrymalis (DQ503458). Therefore, we removed these three sequences from subsequent analyses.