CPR, cuticular protein(s) with the R&R Consensus; DPE,
downstream promoter element; EST, expressed sequence tag; INR,
initiator element; Ka/Ks, ratio of nonsynonymous to synonymous
substitutions; PCA, principal components analysis; qPCR, quantitative
polymerase chain reaction with DNA template; qRT-PCR, quantitative
reverse transcriptase PCR; RACE, rapid amplification of cDNA ends;
R&R Consensus, Rebers and Riddiford Consensus; RR-1, RR-2, two
classes of CPR proteins; UTR, untranslated region of an mRNA; SLAC,
single-likely-ancestor counting method.
All of the authors contributed to the annotation. RSC and JHW wrote
the manuscript; TT directed the experimental work on gene verification
aided by ACE; RSC carried out the phylogenetic and other sequence
analyses; WAD implemented data management. NH contributed unpublished
data on proteomics. The project was conceived and coordinated by JHW.
All authors have read and approved the final version of this manuscript.
The authors appreciate the help Maureen E. Hillenmeyer and Frank
Collins (Notre Dame) provided with the initial stages of annotation and
thank Kathryn Cambell (FlyBase) for input on the genes on 2L. Christos
Louis (Institute of Molecular Biology and Biotechnology, Crete) gave
guidance on naming genes, and Martin Hammond provided help with moving
data to ENSEMBL. Nora Besansky (Notre Dame) shared insight into the
importance of the 2La inversion. Hugh Robertson (Univ. of Illinois)
provided helpful comments on an early draft of the MS. This work was
supported by a grant from the National Institutes of Health (AI55624)