Vertebrate exon trapping methods: implications for transcript mapping withmosquito DNA

Exon trapping methods have played an important role in the development of t ranscript maps. In one in vivo vertebrate method, exons in a genomic DNA cl one are transcribed, and they are recovered without any a priori informatio n on the nature of the expressed transcript. The only requirement is that t he genomic DNA clone contains exons separated by intervening introns that a re removed by splicing during mRNA transcription and that the splice donor and acceptor site sequences follow those used by vertebrates. It is not kno wn whether invertebrate splice donor and acceptor sites from genes that con tain short introns will be processed correctly using an in vivo vertebrate exon trapping method. In this report, an analysis of mosquito splice sites using software designed to identify exons in genomic DNA sequence suggested that the vertebrate exon trapping method could recognize mosquito introns and exons. When a mosquito genomic DNA clone containing the D7 gene was tes ted experimentally, this method failed to recognize and process small intro ns (<63 bp) faithfully. In spite of this failure, exons and exon fragments were recovered. The implications of these findings and their application to map-based positional cloning in mosquito genomics is discussed. (C) 1999 E lsevier Science Ltd. All rights reserved.