Analysis of fragment homology among DNA sequences from cytochrome P450 families 4 and 6

Cytochrome P450s comprise a diverse superfamily of proteins that often shar e as little as 12% amino acid identity. Accordingly, the identification of novel gene families, subfamilies and alleles has been based primarily on 'b enchmark' levels of global amino acid identity and, more recently, phylogen etic relatedness has been used to resolve ambiguous relationships. However, PCR-based cloning strategies have resulted in a large increase in the numb er of short DNA sequences, particularly among insects. Many of these fragme nts remain unnamed and even their gene family membership remains unknown du e to the uncertainty as to whether these fragments accurately reflect the l evels of sequence identity or patterns of evolutionary divergence exhibited by groups of full-length P450 sequences. As a result, the nature of P450 d iversity among insects remains obscure. In this paper, P450 sequences belon ging to the two major gene families, that is, families CYP4 and CYP6, are a nalyzed by comparing segments to full-length sequences. A parameter called the Segmental Divergence Index is used to characterize segments of P450s wi th respect to the degree to which they mirror the divergence of full-length sequences. The reliability of these fragments in phylogenetic analyses is also tested. The results of these analyses support the use of some commonly amplified P450 gene fragments for naming new P450 genes and for studies of P450 diversity and evolution.