ArticleGenome biology2002
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome.
Article in Genome biology, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers, 1 of them a synthesis that pooled it.
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75 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Annotation of the Drosophila melanogaster euchromatic genome: a systematic review.Genome biology · 2002Pooled it
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- Conserved Noncoding Elements Influence the Transposable Element Landscape in Drosophila.Genome biology and evolution · 2018Article
- A New Reference Genome Assembly for the MicrocrustaceanG3 (Bethesda, Md.) · 2017Article
- Neuronal cell fate specification by the molecular convergence of different spatio-temporal cues on a common initiator terminal selector gene.PLoS genetics · 2017Article
- Feature co-localization landscape of the human genome.Scientific reports · 2016Article
- cis-regulatory analysis of the Drosophila pdm locus reveals a diversity of neural enhancers.BMC genomics · 2015Article
- Genomics of ecological adaptation in cactophilic Drosophila.Genome biology and evolution · 2014Article
- Medium-sized tandem repeats represent an abundant component of the Drosophila virilis genome.BMC genomics · 2013Article
- Gene alterations at Drosophila inversion breakpoints provide prima facie evidence for natural selection as an explanation for rapid chromosomal evolution.BMC genomics · 2012Article
- Rate of amino acid substitution is influenced by the degree and conservation of male-biased transcription over 50 myr of Drosophila evolution.Genome biology and evolution · 2012Article
- Theory of the origin, evolution, and nature of life.Life (Basel, Switzerland) · 2011Article
- Formation of regulatory modules by local sequence duplication.PLoS computational biology · 2011Article
- High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation.Genome research · 2011Article
- The evolution of tRNA genes in Drosophila.Genome biology and evolution · 2010Article
- Patterns of DNA-sequence divergence between Drosophila miranda and D. pseudoobscura.Journal of molecular evolution · 2009Article
15 more citing papers are in PubMed but not listed here.
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17 authors.
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Abstract
backgroundIt is widely accepted that comparative sequence data can aid the functional annotation of genome sequences; however, the most informative species and features of genome evolution for comparison remain to be determined.
resultsWe analyzed conservation in eight genomic regions (apterous, even-skipped, fushi tarazu, twist, and Rhodopsins 1, 2, 3 and 4) from four Drosophila species (D. erecta, D. pseudoobscura, D. willistoni, and D. littoralis) covering more than 500 kb of the D. melanogaster genome. All D. melanogaster genes (and 78-82% of coding exons) identified in divergent species such as D. pseudoobscura show evidence of functional constraint. Addition of a third species can reveal functional constraint in otherwise non-significant pairwise exon comparisons. Microsynteny is largely conserved, with rearrangement breakpoints, novel transposable element insertions, and gene transpositions occurring in similar numbers. Rates of amino-acid substitution are higher in uncharacterized genes relative to genes that have previously been studied. Conserved non-coding sequences (CNCSs) tend to be spatially clustered with conserved spacing between CNCSs, and clusters of CNCSs can be used to predict enhancer sequences.
conclusionsOur results provide the basis for choosing species whose genome sequences would be most useful in aiding the functional annotation of coding and cis-regulatory sequences in Drosophila. Furthermore, this work shows how decoding the spatial organization of conserved sequences, such as the clustering of CNCSs, can complement efforts to annotate eukaryotic genomes on the basis of sequence conservation alone.
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