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. 2008 Jan 18;4(1):e3. doi: 10.1371/journal.pgen.0040003

Figure 1. An Example Illustrating the Detection of New Genes.

Figure 1

(A) The probe LD47348 (CG10595) detected two signals in the clade of D. yakuba-santomea-teissieri while only detecting one signal in other species. The new additional signal suggests a new gene candidate.

(B) Southern hybridization results further confirm the extra copy in the D. yakuba-santomea-teissieri clade (M is 1-kb extension marker [Invitrogen]). Lanes 1–8 correspond to Xho I digested DNAs of D. yakuba, D. teissieri, D. santomea, D. erecta, D. melanogaster, D. simulans, D. mauritiana, and D. sechellia, respectively).

(C) Cartoon figure displaying the gene structures of the parental gene (d, or CG10595) and the new duplicate (d-r). The duplicated region is indicated by vertical dash lines. d-r recruited one upstream exon as indicated by yellow box.

(D) Expression patterns of the parental gene. (E) expression patterns of the new gene d-r revealed by one round of RT-PCR and a second round of nested PCR (M indicates DL2000 DNA molecular marker (Takara); E+, E−, L2+, L2−, L3+, L3−, P+, P−, A+, and A− correspond to positive and negative reactions for embryos, second instar larvae, third instar larvae, pupae, and adults, respectively). From these gels, it is clear that d-r is only expressed in the third instar larvae while the parental copy is expressed ubiquitously. All the bands in the negative control lanes are primer dimer bands. E+ and L3+ are weak but clearly visible.