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.