The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin

doi:10.1126/science.1139815

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Science 15 June 2007:
Vol. 316. no. 5831, pp. 1586 - 1591
DOI: 10.1126/science.1139815

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Research Articles

The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin

Christopher D. Smith¹^,2, ShengQiang Shu³, Christopher J. Mungall³ and Gary H. Karpen²^,4^*

¹ Department of Biology, San Francisco State University, San Francisco, CA 94132, USA.
² Drosophila Heterochromatin Genome Project, Department of Genome and Computational Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
³ National Center for Biomedical Ontology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
⁴ Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA 94720, USA.

Fig. 1. Computational pipeline results used for the Release 5.1 annotation. An Apollo (36) screenshot of the evidence (black region) and Release 5.1 annotations (light blue region) for scaffold CP000218, which was produced by merging, extending, and finishing the Release 3 WGS scaffolds (AABU01002750 and AABU010027230) (9). New cDNA evidence was used to merge the Release 3.2b annotations CG40067, CG17443, and CG40109 into one Release 5.1 gene (CG41520) and to identify an alternative exon for CG41250-RB (asterisk). ncRNA CG40375 is shown on the opposite strand to illustrate that it is nested within CG41520. CG40388 represents a Release 3.2b gene that is now annotated as a TE fragment. Complete annotation and evidence are shown in (11). [View Larger Version of this Image (39K GIF file)]

Fig. 2. Evidence of D. melanogaster heterochromatin protein-coding gene annotations. Venn diagrams show the percentage of protein-coding genes supported by gene prediction (pink), EST or cDNA (yellow), and/or BLASTX/TBLASTN comparative genomic evidence (blue). (A) Multi-exon genes are likely to be complete, whereas (B) single-exon genes are likely to represent genes that are fragmented across multiple scaffolds. The number of genes measured for each class are indicated, as well as the number and percent of genes with putative orthologs in melanogaster group species, nonmelanogaster group Drosophilids, or other insect species. [View Larger Version of this Image (27K GIF file)]

Fig. 3. Comparative analysis summary for D. melanogaster heterochromatin genes. (A) Number of heterochromatin protein-coding genes with a predicted ortholog in a given species, ordered (left to right) by increasing evolutionary distance from D. melanogaster. (B) Frequency histograms showing the percentage of heterochromatin protein-coding genes with a predicted ortholog in the 16 insect species tested. (C) Scatter plots of intron lengths (bp) for euchromatin and heterochromatin protein-coding gene introns conserved in either D. erecta or D. virilis. Each data point refers to a single conserved intron. Correlation coefficients (r) for intron lengths are indicated. [View Larger Version of this Image (48K GIF file)]

Fig. 4. Density of repeat and gene features across the heterochromatin. The average percentages of indicated annotation types are shown for each chromosome region (total length in boxes below the x axis). Euchromatin is an average of the noncentric regions of arms 2, 3, and X only. 2Lh, 2Rh, 3Lh, 3Rh, and Xh describe heterochromatic regions that are contiguous with the chromosome arms, whereas the Het regions are mapped to arms and ordered, but not necessarily in the correct orientation (8, 9). The average percentages of sequences for LTR- and LINE-like retrotransposons (red), DNA transposons (green), other and unknown repeats (blue), and TRF tandem repeats and satellite sequences (gray) are indicated. The average number of genes per 100 kb is shown above each histogram. [View Larger Version of this Image (27K GIF file)]

Fig. 5. Overrepresented GO terms in heterochromatin versus euchromatin genes. The percentages of GO molecular-function domains for genes in heterochomatin (red) and euchromatin (blue) are shown. Numbers in parentheses indicate the actual number of domains in heterochromatin. P-value significance scores are shown to the right. Complete GO analyses are presented in the SOM text. [View Larger Version of this Image (26K GIF file)]