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Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotat...

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Autores principales: Misra, Sima, Crosby, Madeline A, Mungall, Christopher J, Matthews, Beverley B, Campbell, Kathryn S, Hradecky, Pavel, Huang, Yanmei, Kaminker, Joshua S, Millburn, Gillian H, Prochnik, Simon E, Smith, Christopher D, Tupy, Jonathan L, Whitfield, Eleanor J, Bayraktaroglu, Leyla, Berman, Benjamin P, Bettencourt, Brian R, Celniker, Susan E, de Grey, Aubrey DNJ, Drysdale, Rachel A, Harris, Nomi L, Richter, John, Russo, Susan, Schroeder, Andrew J, Shu, ShengQiang, Stapleton, Mark, Yamada, Chihiro, Ashburner, Michael, Gelbart, William M, Rubin, Gerald M, Lewis, Suzanna E
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2002
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151185/
https://www.ncbi.nlm.nih.gov/pubmed/12537572
http://dx.doi.org/10.1186/gb-2002-3-12-research0083
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author Misra, Sima
Crosby, Madeline A
Mungall, Christopher J
Matthews, Beverley B
Campbell, Kathryn S
Hradecky, Pavel
Huang, Yanmei
Kaminker, Joshua S
Millburn, Gillian H
Prochnik, Simon E
Smith, Christopher D
Tupy, Jonathan L
Whitfield, Eleanor J
Bayraktaroglu, Leyla
Berman, Benjamin P
Bettencourt, Brian R
Celniker, Susan E
de Grey, Aubrey DNJ
Drysdale, Rachel A
Harris, Nomi L
Richter, John
Russo, Susan
Schroeder, Andrew J
Shu, ShengQiang
Stapleton, Mark
Yamada, Chihiro
Ashburner, Michael
Gelbart, William M
Rubin, Gerald M
Lewis, Suzanna E
author_facet Misra, Sima
Crosby, Madeline A
Mungall, Christopher J
Matthews, Beverley B
Campbell, Kathryn S
Hradecky, Pavel
Huang, Yanmei
Kaminker, Joshua S
Millburn, Gillian H
Prochnik, Simon E
Smith, Christopher D
Tupy, Jonathan L
Whitfield, Eleanor J
Bayraktaroglu, Leyla
Berman, Benjamin P
Bettencourt, Brian R
Celniker, Susan E
de Grey, Aubrey DNJ
Drysdale, Rachel A
Harris, Nomi L
Richter, John
Russo, Susan
Schroeder, Andrew J
Shu, ShengQiang
Stapleton, Mark
Yamada, Chihiro
Ashburner, Michael
Gelbart, William M
Rubin, Gerald M
Lewis, Suzanna E
author_sort Misra, Sima
collection PubMed
description BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations.
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spelling pubmed-1511852003-03-13 Annotation of the Drosophila melanogaster euchromatic genome: a systematic review Misra, Sima Crosby, Madeline A Mungall, Christopher J Matthews, Beverley B Campbell, Kathryn S Hradecky, Pavel Huang, Yanmei Kaminker, Joshua S Millburn, Gillian H Prochnik, Simon E Smith, Christopher D Tupy, Jonathan L Whitfield, Eleanor J Bayraktaroglu, Leyla Berman, Benjamin P Bettencourt, Brian R Celniker, Susan E de Grey, Aubrey DNJ Drysdale, Rachel A Harris, Nomi L Richter, John Russo, Susan Schroeder, Andrew J Shu, ShengQiang Stapleton, Mark Yamada, Chihiro Ashburner, Michael Gelbart, William M Rubin, Gerald M Lewis, Suzanna E Genome Biol Research BACKGROUND: The recent completion of the Drosophila melanogaster genomic sequence to high quality and the availability of a greatly expanded set of Drosophila cDNA sequences, aligning to 78% of the predicted euchromatic genes, afforded FlyBase the opportunity to significantly improve genomic annotations. We made the annotation process more rigorous by inspecting each gene visually, utilizing a comprehensive set of curation rules, requiring traceable evidence for each gene model, and comparing each predicted peptide to SWISS-PROT and TrEMBL sequences. RESULTS: Although the number of predicted protein-coding genes in Drosophila remains essentially unchanged, the revised annotation significantly improves gene models, resulting in structural changes to 85% of the transcripts and 45% of the predicted proteins. We annotated transposable elements and non-protein-coding RNAs as new features, and extended the annotation of untranslated (UTR) sequences and alternative transcripts to include more than 70% and 20% of genes, respectively. Finally, cDNA sequence provided evidence for dicistronic transcripts, neighboring genes with overlapping UTRs on the same DNA sequence strand, alternatively spliced genes that encode distinct, non-overlapping peptides, and numerous nested genes. CONCLUSIONS: Identification of so many unusual gene models not only suggests that some mechanisms for gene regulation are more prevalent than previously believed, but also underscores the complex challenges of eukaryotic gene prediction. At present, experimental data and human curation remain essential to generate high-quality genome annotations. BioMed Central 2002 2002-12-31 /pmc/articles/PMC151185/ /pubmed/12537572 http://dx.doi.org/10.1186/gb-2002-3-12-research0083 Text en Copyright © 2002 Misra et al., licensee BioMed Central Ltd
spellingShingle Research
Misra, Sima
Crosby, Madeline A
Mungall, Christopher J
Matthews, Beverley B
Campbell, Kathryn S
Hradecky, Pavel
Huang, Yanmei
Kaminker, Joshua S
Millburn, Gillian H
Prochnik, Simon E
Smith, Christopher D
Tupy, Jonathan L
Whitfield, Eleanor J
Bayraktaroglu, Leyla
Berman, Benjamin P
Bettencourt, Brian R
Celniker, Susan E
de Grey, Aubrey DNJ
Drysdale, Rachel A
Harris, Nomi L
Richter, John
Russo, Susan
Schroeder, Andrew J
Shu, ShengQiang
Stapleton, Mark
Yamada, Chihiro
Ashburner, Michael
Gelbart, William M
Rubin, Gerald M
Lewis, Suzanna E
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title_full Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title_fullStr Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title_full_unstemmed Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title_short Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
title_sort annotation of the drosophila melanogaster euchromatic genome: a systematic review
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC151185/
https://www.ncbi.nlm.nih.gov/pubmed/12537572
http://dx.doi.org/10.1186/gb-2002-3-12-research0083
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