Genomes differ not only in their TE content but also in the location of their TE insertions, resulting in different maps of occupied and empty loci.
Computational analysis using full-length insertion loci from M. murinus as queries yielded "empty" loci in O. garnetti for npiggy1_Mm and npiggy2_Mm (i.e., the insertion was not present at the presumed orthologous location).
The presence of empty loci (RESites), paralogous to those flanking the identified transposable elements, both autonomous and non-autonomous, as well as the presence of transposon insertion related size polymorphisms, confirmed that some of the mined elements were capable for transposition.
For this (and all other) insertion events, we could verify by PCR that the allelic specificity is conserved in all accessions in which they are found (accessions Pt1, Pt2, Pt3, and Pt9 for Bkb), whereas in the other accessions we could only detect the empty locus.
The tentative alleles were converted to VCF file format (by grouping alleles at each position into a locus, and, since VCF requires all alleles to be non-empty, loci that would otherwise involve an allele being a string of zero nucleotides [e.g., indels] were grown to include one more upstream nucleotide on the + strand, in the usual way for VCF).
We then amplified these 21 mPing-empty loci from the mutator-phenotype and its eight S1 progeny individuals, and we found that in all cases, only smaller-sized PCR products consistent with lacking of mPing in these plants were amplified (data not shown).
In addition, by taking advantage of the draft genome sequence of the indica rice cultivar 93 11 [ 38], locus-specific primers were designed for each of the loci, and the corresponding putative " mPing-empty loci" were also amplified from the donor seed-plant, and sequenced (Additional file 2).
To search for orthologous empty sites, four loci from four silkworm Spy families in three domesticated silkworm strains (DaZao, BiBo, and HeiGao) were assayed by polymerase chain reaction (PCR) with primer pairs flanking each element followed by DNA sequencing.
All the loci were empty in the tested colonies, apart from one corresponding to a copy of AgaP15 which also appears to be occupied in the VK-per sample.
It is not clear why the introduction of a control empty vector at ADE2 locus in BWP17 shortened its lifespan (Fig. S4A).
Of the 52 previously described RGP's [3], PA7 has genes in 33 of the loci, while 19 are empty in PA7.
