An intact copy was defined as a sequence whose length was at least 99% of the length of the longest copy detected, and a partial IS was defined as a >500 bp fragment with >80% DNA identity to an intact copy.
We noticed that the longest copy that could represent the initial deleted progenitor is more than 1700 bp long.
The longest copy (112) is 9021-bp long, including TIRs of 4246-bp and 4680-bp (5′ and 3′, respectively; see Additional file 1).
All clean reads were assembled into transcripts by Trinity software; and the longest copy of redundant transcripts was regarded as a unigene [ 28, 29].
First, we expected that the longest copy detected and the reference copy would have the same size because insertions in genomic copies (as compared to the reference copy) were not taken into account in the computation of the copy size.
For four other families (Osr22, Osr31, Osr38 and RIRE1), however, the longest copy detected is more than 5% shorter than the reference copy, which suggests that this copy was not detected by our search.
DpcCYC1 is the longest copy, with fewer gaps in the intervening region (suggesting these sequences may be less diverged from each other than the other copies), followed by DpcCYC2A.
For 6 families (Hopi/Osr27, Osr2, Osr8, Osr20, Osr34 and Osr44), the slight difference in size between the longest copy and the reference copy (99.3 to 99.9% of the reference copy size) is due to the homogenization of the two LTRs in the reference copy (see Material and Methods).
If a gene in the reference pool was not found in all of the analyzed genomes, the longest copy of the gene was re-BLASTed against the Newbler assemblies of each of the genomes in which the gene was initially not found.
