Genomic organization, polymorphisms and molecular evolution of the goose-type lysozyme gene from Zhikong scallop Chlamys farreri

Abstract

Lysozyme is a ubiquitous hydrolase that plays an important role in protecting the host against pathogenic infection. In the present study, the genomic DNA sequence of an invertebrate goose type (G type) lysozyme (designated CfLysG) was cloned from Zhikong scallop Chlamys farreri by genome walking technique. The full-length DNA of CfLysG gene was of 9455bp, and the fragment from the transcription site to the polyadenylation site was of 8217bp. A total of 104 SNPs and 29 ins–del polymorphisms were identified in the genomic sequence of CfLysG, and most of them were located in the promoter and intron regions, except for three SNPs located in the exon regions. Some putative transcription factor binding sites in the promoter region suggested the involvement of CfLysG in immune responses. There were six exons of 55, 60, 90, 113, 145 and 140bp interrupted by five relatively large introns in the genomic DNA sequence. CfLysG exhibited a unique exon–intron organization which was different from both its vertebrate and invertebrate homologues. Though some introns were lost in the urochordate homologues, four of the five introns in CfLysG DNA shared homologous positions with vertebrate G type lysozyme genes, which indicated the existence of these introns in the ancestry of G type lysozyme. With respect to the number and size of both exons and introns, the gene organization of CfLysG was more similar to that of vertebrate G type lysozyme, but its amino acid sequence shared higher similarity with that of other invertebrate G type lysozymes. In the phylogenic tree, G type lysozymes from mollusk were clustered together and formed a sister clade to the urochordate and vertebrate G type lysozymes. G type lysozyme was separated from C and I type lysozymes and closely matched to the phage-type lysozyme. The results suggested that G type lysozyme might be evolutionarily closest to the lysozyme ancestor, and they would be helpful to understand the evolution of lysozyme genes.