SDH genes on chromosome 1 (md1) and chromosome 7 (md7) in M. domestica were highly duplicated by tandem duplication (Table 2), in contrast to the other Rosaceae species (P. mume, P. persica).
From these data, it was apparent that many of the potential gains and losses we detected were actually the result of differential loss of ancestrally duplicated genes from the yeast whole-genome duplication (Table 5), a process that contributes to reproductive isolation (Lynch and Conery 2000; Scannell et al. 2006).
In our analysis, the ABCB1-ABCB2 showed a relatively recent duplication (with low Ks), and more important, the ancestral state may have shown both expression patterns of the descendants prior to duplication (Table 4), therefore, this pair is the most probable duplicates for subfunctionalization.
Four loci found to be duplicated in one or more test species according to aCGH were chosen for quantitative PCR (qPCR) validation for their observed duplication patterns- one duplicated in all species relative to A. burtoni, two duplicated in all three Lake Malawi radiation species and one species-specific duplication (Table 2).
Amino acid sequences within the insertion grouped into 3 patterns flanked by various sequences due to the target site duplication (Table 2).
All showed canonical piggyBac TTAA sequence duplication (Table S1), although the second integration site in strain C could not be resolved.
PCR and sequencing at the tandem duplication boundary confirmed that domesticus mice from Germany (100%) and France (25%) and a single castaneus mouse from Taiwan (12.5%) had the duplication (Table 1).
We confirmed the presence of this duplication using real time PCR to quantify genomic DNA template near the predicted ends of the duplication (Table S2) and subsequently used PCR with primers directed across the predicted duplication; such primers would only produce a product in the presence of a tandem duplication (reverse primers P3 or P4 and forward P11, see Figure 1 and Table S2).
Concerning the right HG number, 120 (60.6 %) had a single HG and 78 (39.4 %) a duplication (Table 1a).
The smallest CNV was 30kbs in length and demonstrated a single copy duplication (Table 4).
