Structure and polymorphism of the Chironomus thummi gene encoding special lobe-specific silk protein, ssp160

cDNA encoding Chironomus thummi ssp160 was used to isolate a genomic clone that hybridized in situ to band A2b on polytene chromosome IV, the site of the ssp160 gene. DNA sequencing, primer extension and gene/cDNA nucleotide sequence alignment revealed the gene contains six exons and five introns; 7 0% of ssp160 is encoded in exon 3. Variations between cDNA and gene sequenc es led to the design of a polymerase chain reaction, restriction fragment l ength polymorphism assay that was subsequently used to demonstrate the exis tence of polymorphic alleles whose distribution varied between geographical ly separated populations of larvae. The polymorphism is associated with cod on deletions in a six-amino-acid repeat containing an N-linked glycosylatio n motif. These deletions may have resulted from slipped-strand mispairing d uring DNA replication. (C) 1998 Elsevier Science B.V. All rights reserved.