Selection of ultraconserved elements
Iterative inclusion of additional genomes resulted in the selection of
553, 1,649 and 4,040 UCEs that are shared among 7, 6 and 5 genomes,
respectively. (Any set of 5 genomes includes both bivalve and gastropod
genomes.) After filtering candidate UCEs to mask regions with repeated
motives, low-level complexity or a length <100 nt, we retained
388, 1,257 and 3,366 UCEs (5,011 in total) for 7, 6 and 5 genomes,
respectively. Further filtering and overlap detection (within UCEs and
to ORFs) resulted in the retention of 4,107 UCEs, which jointly cover
595,060 nt.