In addition to EFNB1, the duplication interval included two other entirely duplicated genes, PJA1 encoding the RING-finger protein Praja1 and STARD8, which encodes a cell junction protein.
We found that 44% of the WSSD duplication intervals (33.4/75.8 Mb) were not detected by the genome assembly based comparison and, likely represent collapsed duplications (Fig. 1).
Lethality in the first interval is lower in the duplication mutants compared with the deletion mutants because essential genes cannot be lost in a duplication.
The numbers of genes involved in the duplication events are given in parentheses.
The transposon insertion in the essential gene is maintained only in the duplication derivatives.
Seventy-six percent (778/1020) of the bovine segmental duplication intervals identified by both WGAC and WSSD correspond to complete or partial gene duplications (See Additional File 1: Table S3).
Comparative genome hybridization has identified a hemizygous 78 Kbp duplication in the mapped interval.
Such major disorders include VCFS/DGS, the reciprocal duplication in the same interval, and cat-eye syndrome, a partial tetrasomy [ 5- 12].
Following previous studies [ 7], we defined segmental duplications based on the union of significant WGAC hits with less than 94% sequence identity and WSSD results (Fig. 1): i.e. WGAC duplication intervals that were greater than ≥ 94% sequence identity and ≥ 10 kb in size but not supported by WSSD, were excluded from the genome-wide calculation of segmental duplications.
After confirming that duplication events in the youngest interval of 0 ≤ dS < 0.2 are much more abundant than those in the other two intervals (0.2 ≤ dS < 0.4 and 0.4 ≤ dS < 0.6) for most of the species, we further subdivided this youngest class with the boundaries dSs = 0.01, 0.03, and 0.1 to get a finer view of the age dependence.
In literature, the duplication of elements is pointed out as the main reason.
