Identification of One Intron Loss and Phylogenetic Evolution of Dfak Gene in the Drosophila melanogaster Species Group

Abstract

Intron loss and its evolutionary significance have been noted in Drosophila. The current study provides another example of intron loss within a single-copy Dfak gene in Drosophila. By using polymerase chain reaction (PCR), we amplified about 1.3 kb fragment spanning intron 5-10, located in the position of Tyr kinase (TyK) domain of Dfak gene from Drosophila melanogaster species group, and observed size difference among the amplified DNA fragments from different species. Further sequencing analysis revealed that D. melanogaster and D. simulans deleted an about 60 bp of DNA fragment relative to other 7 Drosophila species, such as D. elegans, D. ficusphila, D. biarmipes, D. takahashii, D. jambulina, D. prostipennis and D. pseudoobscura, and the deleted fragment located precisely in the position of one intron. The data suggested that intron loss might have occurred in the Dfak gene evolutionary process of D. melanogaster and D. simulans of Drosophila melanogaster species group. In addition, the constructed phylogenetic tree based on the Dfak TyK domains clearly revealed the evolutionary relationships between subgroups of Drosophila melanogaster species group, and the intron loss identified from D. melanogaster and D. simulans provides a unique diagnostic tool for taxonomic classification of the melanogaster subgroup from other group of genus Drosophila.

Intron exclusion and the mystery of intron loss

“…Long intron might prevent such an HR. Interestingly, the reported intron exclusion all occur with short intron [16–18]. Interestingly, the introns that are found excluded in this study are generally short except for conifer Adh intron 1 (Fig.…”

“…Genome‐wide comparison of intron positions revealed five exact losses of a single internal intron in five genes of mouse, and one such in‐frame loss of an internal intron in rat [16]. Intron Y, which should be located between the intron 7 and 8, was reported to be lost precisely from Dfak of Drosophila melanogaster group [17]. Feiber et al [18] showed that there is an intron presence‐absence polymorphism for the 4f‐rnp gene among Drosophila robusta population in which intron 7 is deleted precisely with the upstream and downstream introns intact.…”

Structural and Comparative Analyses of Insects Suggest the Presence of an Ultra-Conserved Regulatory Element of the Genes Encoding Vacuolar-Type ATPase Subunits and Assembly Factors

“…Formally, the gene replacement event described above represents a case of intron exclusion through cDNA-directed homologous recombination, which has already been described in D. melanogaster [ 64 , 65 ]. Intron exclusion is an important evolutionary process in which homologous recombination events occur between the cDNA generated via retroposition and its genomic, intron-containing locus, resulting in the generation of an intron-free gene.…”

“…One of these copies (Dvir\GJ10919) was replaced by a retroposed copy (depicted as C' in Figure 6), whereas the other one (Dvir\GJ22513) retained the structure and possibly the function of the ancestral gene (shown as the structural and functional ortholog in Figure 6). Formally, the gene replacement event described above represents a case of intron exclusion through cDNA-directed homologous recombination, which has already been described in D. melanogaster [64,65]. Intron exclusion is an important evolutionary process in which homologous recombination events occur between the cDNA generated via retroposition and its genomic, intron-containing locus, resulting in the generation of an intron-free gene.…”

Cloning, comparative characterization of porcine SCAP gene, and identification of its two splice variants

“…Similar intron losses have been reported in Xy species. For example, a small intron of the Dfak gene is absent from Drosophila melanogaster and D. simulans, but it remains intact in other species of the D. melanogaster species group (Jin et al 2005). Earlier studies by Feiber et al (2002) showed certain intron losses in the 4f-rnp gene in members of a D. melanogaster population.…”