Genome Biology | Article collections | Release 3 of the Drosophila genome

Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen Genome Biology 2002, 3:research0085-0085.16 (31 December 2002)

Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.

Annotation of the Drosophila melanogaster euchromatic genome: a systematic review

Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis et al. Genome Biology 2002, 3:research0083-0083.22 (31 December 2002)

The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.

Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome

Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002)

Analysis of 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.

Systematic determination of patterns of gene expression during Drosophila embryogenesis

Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002)

As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker Genome Biology 2002, 3:research0084-0084.20 (23 December 2002)

Using Release 3 of the euchromatic genomic sequence of Drosophila melanogaster, 85 known and eight novel families of transposable element have been identified, varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence.

Apollo: a sequence annotation editor

SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002)

Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome.

An integrated computational pipeline and database to support whole-genome sequence annotation

CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002)

In the course of annotating the Drosophila melanogaster genome sequence, several new open-source software tools and a database schema to support large-scale genome annotation were developed and integrated in to a reusable software system for whole-genome annotation.

A Drosophila full-length cDNA resource

Mark Stapleton, Joe Carlson, Peter Brokstein, Charles Yu, Mark Champe, Reed George, Hannibal Guarin, Brent Kronmiller, Joanne Pacleb, Soo Park, Ken Wan, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0080-0080.8 (23 December 2002)

High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the Drosophila Gene Collection has been generated and compared to the annotated Release 3 genomic sequence. More than 5,300 cDNAs have been identifieed that contain a complete and accurate protein-coding sequence, corresponding to at least one splice form for 40% of the predicted D. melanogaster genes.

Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence

Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin et al. Genome Biology 2002, 3:research0079-0079.14 (23 December 2002)

The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence quality and validate the assembly.

Computational analysis of core promoters in the Drosophila genome

Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002)

Candidate transcription start sites have been identified for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of the sequences flanking these candidate transcription start sites revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE).

		Research Heterochromatic sequences in a Drosophila whole-genome shotgun assembly Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen Genome Biology 2002, 3:research0085-0085.16 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Annotation of an improved whole-genome shotgun assembly of the Drosophila melanogaster genome predicted 297 protein-coding genes and six non-protein-coding genes, including known heterochromatic genes, and regions of similarity to known transposable elements. Fluorescence in situ hybridization was used to correlate the genomic sequence with the cytogenetic map; the annotated euchromatic sequence extends into the centric heterochromatin on each chromosome arm.
		Research Annotation of the Drosophila melanogaster euchromatic genome: a systematic review Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis et al. Genome Biology 2002, 3:research0083-0083.22 (31 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The recent completion of the Drosophila melanogaster genomic sequence to high quality, and the availability of a greatly expanded set of Drosophila cDNA sequences, afforded FlyBase the opportunity to significantly improve genomic annotations.
		Research Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0086-0086.20 (30 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Analysis of 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.
		Research Systematic determination of patterns of gene expression during Drosophila embryogenesis Pavel Tomancak, Amy Beaton, Richard Weiszmann, Elaine Kwan, ShengQiang Shu, Suzanna E Lewis, Stephen Richards, Michael Ashburner, Volker Hartenstein, Susan E Celniker, Gerald M Rubin Genome Biology 2002, 3:research0088-0088.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary As a first step to creating a comprehensive atlas of gene-expression patterns during Drosophila embryogenesis, 2,179 genes have been examinded by in situ hybridization to fixed Drosophila embryos. Of the genes assayed, 63.7% displayed dynamic expression patterns that were documented with 25,690 digital photomicrographs of individual embryos.
		Research The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker Genome Biology 2002, 3:research0084-0084.20 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Using Release 3 of the euchromatic genomic sequence of Drosophila melanogaster, 85 known and eight novel families of transposable element have been identified, varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence.
		Software Apollo: a sequence annotation editor SE Lewis, SMJ Searle, N Harris, M Gibson, V Iyer, J Richter, C Wiel, L Bayraktaroglu, E Birney, MA Crosby, JS Kaminker, BB Matthews, SE Prochnik, CD Smith, JL Tupy, GM Rubin, S Misra, CJ Mungall, ME Clamp Genome Biology 2002, 3:research0082-0082.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Apollo was developed to enable curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome.
		Software An integrated computational pipeline and database to support whole-genome sequence annotation CJ Mungall, S Misra, BP Berman, J Carlson, E Frise, N Harris, B Marshall, S Shu, JS Kaminker, SE Prochnik, CD Smith, E Smith, JL Tupy, C Wiel, GM Rubin, SE Lewis Genome Biology 2002, 3:research0081-0081.11 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary In the course of annotating the Drosophila melanogaster genome sequence, several new open-source software tools and a database schema to support large-scale genome annotation were developed and integrated in to a reusable software system for whole-genome annotation.
		Research A Drosophila full-length cDNA resource Mark Stapleton, Joe Carlson, Peter Brokstein, Charles Yu, Mark Champe, Reed George, Hannibal Guarin, Brent Kronmiller, Joanne Pacleb, Soo Park, Ken Wan, Gerald M Rubin, Susan E Celniker Genome Biology 2002, 3:research0080-0080.8 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary High-quality full-insert sequence for 8,921 putative full-length cDNA clones in the Drosophila Gene Collection has been generated and compared to the annotated Release 3 genomic sequence. More than 5,300 cDNAs have been identifieed that contain a complete and accurate protein-coding sequence, corresponding to at least one splice form for 40% of the predicted D. melanogaster genes.
		Research Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin et al. Genome Biology 2002, 3:research0079-0079.14 (23 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The Drosophila melanogaster genome was the first metazoan genome to be sequenced by whole-genome shotgun. Now, the sequence has been finished in a process designed to close gaps, improve sequence quality and validate the assembly.
		Research Computational analysis of core promoters in the Drosophila genome Uwe Ohler, Guo-chun Liao, Heinrich Niemann, Gerald M Rubin Genome Biology 2002, 3:research0087-0087.12 (20 December 2002) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Candidate transcription start sites have been identified for about 2,000 Drosophila genes by aligning 5' expressed sequence tags (ESTs) from cap-trapped cDNA libraries to the genome. Examination of the sequences flanking these candidate transcription start sites revealed the presence of well-known core promoter motifs such as the TATA box, the initiator and the downstream promoter element (DPE).

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Release 3 of the Drosophila genome