Comparative validation of the D. melanogaster modENCODE transcriptome annotation

Abstract

Accurate gene model annotation of reference genomes is critical for making them useful. The modENCODE project has improved the D. melanogaster genome annotation by using deep and diverse high-throughput data. Since transcriptional activity that has been evolutionarily conserved is likely to have an advantageous function, we have performed large-scale interspecific comparisons to increase confidence in predicted annotations. To support comparative genomics, we filled in divergence gaps in the Drosophila phylogeny by generating draft genomes for eight new species. For comparative transcriptome analysis, we generated mRNA expression profiles on 81 samples from multiple tissues and developmental stages of 15 Drosophila species, and we performed cap analysis of gene expression in D. melanogaster and D. pseudoobscura. We also describe conservation of four distinct core promoter structures composed of combinations of elements at three positions. Overall, each type of genomic feature shows a characteristic divergence rate relative to neutral models, highlighting the value of multispecies alignment in annotating a target genome that should prove useful in the annotation of other high priority genomes, especially human and other mammalian genomes that are rich in noncoding sequences. We report that the vast majority of elements in the annotation are evolutionarily conserved, indicating that the annotation will be an important springboard for functional genetic testing by the Drosophila community.

Promoter Architecture and Sex-Specific Gene Expression in Daphnia pulex

“…Overall, the distribution of consensus promoter widths observed are consistent with those determined in D. melanogaster using CAGE ( Figure 2A) (Hoskins et al 2011;Chen et al 2014). A proportion of the consensus promoter widths are long, including 1104 (10.4%) with widths longer than 30 bp (Figure 2A).…”

“…However, three of the four overrepresented dinucleotides (GA, GC, and GG) have guanines at 21, which is observed less commonly in metazoans. D. melanogaster, the most closely related species for which CAGE data are available (Hoskins et al 2011;Chen et al 2014), is enriched for YR at [21, +1]; no enrichment of dinucleotides with G at 21 is reported. In human, where core promoters tend to be GC-rich (Fitzgerald et al 2004(Fitzgerald et al , 2006, YR, but no GN dinucleotides, are enriched at initiation sites (Sandelin et al 2007;Frith et al 2008).…”

Comparative transcriptomics across 14 Drosophila species reveals signatures of longevity

“…Overall, the expression profiles were similar to one another, with Spearman correlation coefficients of species pairs ranging between 0.68 and 0.90. Our expression data were also consistent with the previous studies of gene expression across multiple Drosophila species (Chen et al., 2014; Zhang, Sturgill, Parisi, Kumar & Oliver, 2007; Figure S2a).…”

“…We compared our expression data with two previous studies of gene expression across multiple Drosophila species (Chen et al., 2014; Zhang et al., 2007)—GSE99574 is based on RNA‐seq and GSE6640 is based on microarrays (herein referred to as “reference studies”). For simplicity, we used only “male replicate 1” in each reference study for whole‐body expression.…”

Genome comparisons indicate recent transfer ofwRi‐likeWolbachiabetween sister speciesDrosophila suzukiiandD. subpulchrella

“…We used BLAST to identify orthologs in the D. suzukii assembly of Ometto et al. (2013), the unpublished draft D. subpulchrella assembly described above, a D. biarmipes assembly (Chen et al., 2014), and a second‐generation D. simulans assembly (Hu, Eisen, Thornton, & Andolfatto, 2013). Data for H2A and amylase were eliminated because H2A had multiple nonidentical paralogs in each species and homologs of D. melanogaster amylase could not be found in the assemblies.…”