Local Genomic Instability of the Gene Family in the Purple Sea Urchin Inferred from BAC Insert Deletions.

The () gene family in the purple sea urchin, , encodes immune response proteins. The genes are clustered, surrounded by short tandem repeats, and some are present in genomic segmental duplications. The genes share regions of sequence and include repeats in the coding exon. This complex structure is consistent with putative local genomic instability. Instability of the gene cluster was tested by 10 days of growth of harboring bacterial artificial chromosome (BAC) clones of sea urchin genomic DNA with inserts containing genes. After the growth period, the BAC DNA inserts were analyzed for size and gene content. Clones with multiple genes showed a variety of deletions, including loss of one, most, or all genes from the cluster. Alternatively, a BAC insert with a single gene was stable. BAC insert instability is consistent with variations in the gene family composition among sea urchins, the types of genes in the family, and a reduction in the gene copy number in single coelomocytes. Based on the sequence variability among genes within and among sea urchins, local genomic instability of the family may be important for driving sequence diversity in this gene family that would be of benefit to sea urchins in their arms race with marine microbes.