The Genom of Homo sapiens.pdf

WHOLE-GENOME COMPARISONS 279Table 2. Distributions of (Anopheles/D.melanogaster) Ecores in the Sequence of Drosophilain Two Successive AnnotationsEcores Ecores Ecores inBDGP Genes within Exons overlapping genes notannotation Ecores Genes detected genes Exons detected exons in exonsRelease 2 47,134 13,468 11,147 42,633 54,771 31,751 41,332 1072(%) (100) (100) (83) (90.5) (100) (58) (88) (2.5)Release 3 46,742 13,666 11,167 43,705 61,085 33,996 42,679 1026(%) (100) (100) (82) (93.5) (100) (56) (91.5) (2)lease 3 and observed that, at present, all ecores have beenplaced in two gene models (Fig. 3, bottom).Based on remote protein sequence or structure homologies,an additional set of 1,042 D. melanogaster candidategenes has been proposed (Gopal et al. 2001) (http://genomes.rockefeller.edu/dm). Ecores could be found in18.7% of these new gene models (the list of the matchescan be found at www.genoscope.cns/externe/Fly). Thislow fraction of matches could either result from a very lowconservation of these genes between A. gambiae and D.melanogaster, possibly representing a subset of rapidlyevolving genes, or indicate that a large fraction of thesehypothetical genes should be dismissed. However, Exofishcan also serve to validate a number of these potentialgenes. A genome-wide analysis was also performed onthe assembly of the A. gambiae genome sequence draft(Holt et al. 2002). We found more ecores in the Anophelesassembly (54,069 in release 6.01a) than in the D.melanogaster genome (ratio = 1.16). Several explanationsthat are not mutually exclusive may account for thisobservation. The high number of ecores could reflect (1)an increased coding capacity in the genome of Anophelesor (2) a larger number of pseudogenes or unmasked tranposableelements in Anopheles or (3) problems in the sequenceassembly. The presence of at least two differenthaplotypes in the A. gambiae strain sequenced is knownto have introduced a number of redundancies in the assembly,essentially as linked artefactual duplications andunanchored duplicated scaffolds (Holt et al. 2002). Workis in progress to test these hypotheses. We compared theFigure 3. Exofish analysis on a region on arm 2L of the genome of D. melanogaster from 2 different releases of annotations, andaround the same ecores. (Top) Results from release 2 of BDGP. (Bottom) Results from release 3 of BDGP. (A,D) BDGP annotationson the 5´–3´ strand. (B,E) BDGP annotations on the 3´–5´ strand. The genes are represented by boxes, with exons in black and intronsin white. (C,F) Ecores (gray boxes). In release 2 (top), 5 ecores (numbers 7, 8, 9, 11, 12) overlap 4 gene models, and 7 ecores (numbers1, 2, 3, 4, 5, 6, 10) do not overlap any annotation. In release 3, a large gene model overlaps all the ecores that fall exclusively inexons except ecore number 9. This ecore is part of a gene model on the 5´–3´ strand, which is predicted inside an intron on the 3´–5´strand.