ArticleGenome research2007
Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 100 papers.
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Who cites it
100 citing papers in PubMed.
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- Monitoring translation in all reading frames downstream of weak stop codons provides mechanistic insights into the impact of nucleotide and cellular contexts.Nucleic acids research · 2023Article
- An Integrated Approach for Microprotein Identification and Sequence Analysis.Journal of visualized experiments : JoVE · 2022Article
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- IsoMiRmap: fast, deterministic and exhaustive mining of isomiRs from short RNA-seq datasets.Bioinformatics (Oxford, England) · 2021Article
- Comparative genomics of Chlamydomonas.The Plant cell · 2021Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Nature communications · 2021Article
- Tissue-specific dynamic codon redefinition inProceedings of the National Academy of Sciences of the United States of America · 2021Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.Research square · 2020Article
- SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes.bioRxiv : the preprint server for biology · 2020Article
- Emerging role of tumor-related functional peptides encoded by lncRNA and circRNA.Molecular cancer · 2020Review
- Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs.Molecular biology and evolution · 2020Article
- CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500Genome research · 2020Article
- Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci.Genome research · 2019Article
- Predicting functional long non-coding RNAs validated by low throughput experiments.RNA biology · 2019Article
- Multilevel regulation of the glass locus during Drosophila eye development.PLoS genetics · 2019Article
40 more citing papers are in PubMed but not listed here.
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Authors and funding
19 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The availability of sequenced genomes from 12 Drosophila species has enabled the use of comparative genomics for the systematic discovery of functional elements conserved within this genus. We have developed quantitative metrics for the evolutionary signatures specific to protein-coding regions and applied them genome-wide, resulting in 1193 candidate new protein-coding exons in the D. melanogaster genome. We have reviewed these predictions by manual curation and validated a subset by directed cDNA screening and sequencing, revealing both new genes and new alternative splice forms of known genes. We also used these evolutionary signatures to evaluate existing gene annotations, resulting in the validation of 87% of genes lacking descriptive names and identifying 414 poorly conserved genes that are likely to be spurious predictions, noncoding, or species-specific genes. Furthermore, our methods suggest a variety of refinements to hundreds of existing gene models, such as modifications to translation start codons and exon splice boundaries. Finally, we performed directed genome-wide searches for unusual protein-coding structures, discovering 149 possible examples of stop codon readthrough, 125 new candidate ORFs of polycistronic mRNAs, and several candidate translational frameshifts. These results affect >10% of annotated fly genes and demonstrate the power of comparative genomics to enhance our understanding of genome organization, even in a model organism as intensively studied as Drosophila melanogaster.
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