Nonuniform evolution of duplicated, developmentally controlled chorion genes in a silkmoth

We report the sequence of A/B.L1, a tightly linked pair of genes from the A and B chorion families in Bombyx mori. Comparison with the previously characterized A/B.L11 and A/B.L12 pairs from the same species reveals moderate sequence divergence, which is clearly nonuniform. Although the average divergence of A/B.L12 from the other two pairs is more than double that between A/B.L11 and A/B.L1, the ratio differs by more than 30-fold in different DNA regions. One domain of the A gene is highly divergent between A/B.L12 and A/B.L1 or A/B.L11, but essentially invariable in the latter two. In well-aligned DNA segments, nearly all mutated sites (111/112) show variants shared by two of the three sequences, in 42% of the cases between the more distantly related pairs (A/B.L12 and either A/B.L1 or A/B.L11). Eight of the variants shared by distantly related pairs are clustered within 51 bp, suggesting the possibility that they arose through sequence transfers between gene pairs, rather than being primitive or resulting from independent mutations. The short intergenic, putatively regulatory DNA of the developmentally middle A/B.L1 and A/B.L11 pairs resembles that of the late HcA/HcB pairs, particularly in patches that may correspond to cis-regulatory elements.