TABLE 1

List of candidate genes chosen for sequencing in D. simulans and D. yakuba

Codons sequencedNucleotide divergenceb
MEL-SIMMEL-YAK
GeneCodonsENCgf/gs scoresaBLAST hitEST matchSIMYAKdndsdndsIndelc
Candidate genes for rapid evolution
DS07660.145461.0—, 101Phosphate cotransporterNone00
DS06238.421961.030, 63Cuticular proteinNone2062130.01030.16100.01290.2967IF
DS03192.44661.0—, —No matchEmbryo00
DS03192.35761.0—, —No matchHead3939(0.0438)(0.0484)(0.1960)(0.3945)OOF
BACR44L22.424160.6—, —Zn2+ metalloproteaseNone24000.02600.1538
DS01514.339660.6—, 49No matchNone830(0.0280)(0.0160)OOF
Mst35Ba14760.4—, —No matchHead00
DS07108.529560.2— 25Antibacterial proteaseNone00
DS07721.6158559.4—, 271REJ-domain proteinsNone10044550.04940.13740.16870.4302OOFd, IFe
DS04095.130359.3—, 64No matchYes00
DS04095.219158.8—, 53No matchNone00
EG0007.1016957.0— 26No matchEmbryo1681680.01190.08950.05120.3043OOFf
Mst35Bb14755.4—, —No matchHead00
Control genes
BACR44L22.325451.3—, 53Zn2+ metalloprotreaseNone2412410.01190.08950.03210.2586
DS01068.516035.635, 382Immune-related proteinNone00
DS00810.36927.016, 14No matchMany00
  • EG0007.10 is X-linked; all other genes are located on the second chromosome. MEL, D. melanogaster, SIM, D. simulansr, YAK, D. yakuba.

  • a gf, GENEFINDER score; gs, GENSCAN score.

  • b Values in parentheses are for the longest conserved reading frame in coding sequences with out-of-frame indels.

  • c OOF, out-of-frame indel; IF, in-frame indel.

  • d Exon 1 of annotated sequence; probably an incorrectly annotated exon of an otherwise functional protein.

  • e Exon 3 of annotated sequence.

  • f Extending 3′ end of coding sequence in D. erecta.