The Drosophila melanogaster transcriptome by paired-end RNA sequencing

被引：102

作者：

Daines, Bryce ^{[1
,2
]}

Wang, Hui ^{[2
]}

Wang, Liguo ^{[3
]}

Li, Yumei ^{[1
,2
]}

Han, Yi ^{[2
]}

Emmert, David ^{[4
]}

Gelbart, William ^{[4
]}

Wang, Xia ^{[1
,2
]}

Li, Wei ^{[3
,5
]}

Gibbs, Richard ^{[1
,2
]}

Chen, Rui ^{[1
,2
]}

机构：

[1] Baylor Coll Med, Dept Mol & Human Genet, Houston, TX 77030 USA

[2] Baylor Coll Med, Human Genome Sequencing Ctr, Houston, TX 77030 USA

[3] Baylor Coll Med, Dan L Duncan Canc Ctr, Houston, TX 77030 USA

[4] Harvard Univ, Dept Mol & Cellular Biol, Cambridge, MA 02138 USA

[5] Baylor Coll Med, Dept Mol & Cellular Biol, Houston, TX 77030 USA

来源：

GENOME RESEARCH | 2011年 / 21卷 / 02期

关键词：

GENE-EXPRESSION; Y-CHROMOSOME; IDENTIFICATION; GENOME; SEQ;

D O I：

10.1101/gr.107854.110

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

RNA-seq was used to generate an extensive map of the Drosophila melanogaster transcriptome by broad sampling of 10 developmental stages. In total, 142.2 million uniquely mapped 64-100-bp paired-end reads were generated on the Illumina GA II yielding 3563 sequencing coverage. More than 95% of FlyBase genes and 90% of splicing junctions were observed. Modifications to 30% of FlyBase gene models were made by extension of untranslated regions, inclusion of novel exons, and identification of novel splicing events. A total of 319 novel transcripts were identified, representing a 2% increase over the current annotation. Alternate splicing was observed in 31% of D. melanogaster genes, a 38% increase over previous estimations, but significantly less than that observed in higher organisms. Much of this splicing is subtle such as tandem alternate splice sites.

引用

页码：315 / 324

页数：10

共 42 条

[1] MachiBase: a Drosophila melanogaster 5′-end mRNA transcription database [J].

Ahsan, Budrul ;

Saito, Taro L. ;

Hashimoto, Shin-ichi ;

Muramatsu, Keigo ;

Tsuda, Manabu ;

Sasaki, Atsushi ;

Matsushima, Kouji ;

Aigaki, Toshiro ;

Morishita, Shinichi .

NUCLEIC ACIDS RESEARCH, 2009, 37 :D49-D53

[2] Gene expression during the life cycle of Drosophila melanogaster [J].

Arbeitman, MN ;

Furlong, EEM ;

Imam, F ;

Johnson, E ;

Null, BH ;

Baker, BS ;

Krasnow, MA ;

Scott, MP ;

Davis, RW ;

White, KP .

SCIENCE, 2002, 297 (5590) :2270-2275

[3] Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing [J].

Campbell, Peter J. ;

Stephens, Philip J. ;

Pleasance, Erin D. ;

O'Meara, Sarah ;

Li, Heng ;

Santarius, Thomas ;

Stebbings, Lucy A. ;

Leroy, Catherine ;

Edkins, Sarah ;

Hardy, Claire ;

Teague, Jon W. ;

Menzies, Andrew ;

Goodhead, Ian ;

Turner, Daniel J. ;

Clee, Christopher M. ;

Quail, Michael A. ;

Cox, Antony ;

Brown, Clive ;

Durbin, Richard ;

Hurles, Matthew E. ;

Edwards, Paul A. W. ;

Bignell, Graham R. ;

Stratton, Michael R. ;

Futreal, P. Andrew .

NATURE GENETICS, 2008, 40 (06) :722-729

[4] GENECODIS: a web-based tool for finding significant concurrent annotations in gene lists [J].

Carmona-Saez, Pedro ;

Chagoyen, Monica ;

Tirado, Francisco ;

Carazo, Jose M. ;

Pascual-Montano, Alberto .

GENOME BIOLOGY, 2007, 8 (01)

[5] Y chromosomal fertility factors kl-2 and kl-3 of Drosophila melanogaster encode dynein heavy chain polypeptides [J].

Carvalho, AB ;

Lazzaro, BP ;

Clark, AG .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (24) :13239-13244

[6] Y chromosome and other heterochromatic sequences of the Drosophila melanogaster genome:: how far can we go? [J].

Carvalho, AB ;

Vibranovski, MD ;

Carlson, JW ;

Celniker, SE ;

Hoskins, RA ;

Rubin, GM ;

Sutton, GG ;

Adams, MD ;

Myers, EW ;

Clark, AG .

GENETICA, 2003, 117 (02) :227-237

[7] Identification of five new genes on the Y chromosome of Drosophila melanogaster [J].

Carvalho, AB ;

Dobo, BA ;

Vibranovski, MD ;

Clark, AG .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2001, 98 (23) :13225-13230

[8] Evolution of genes and genomes on the Drosophila phylogeny [J].

Clark, Andrew G. ;

Eisen, Michael B. ;

Smith, Douglas R. ;

Bergman, Casey M. ;

Oliver, Brian ;

Markow, Therese A. ;

Kaufman, Thomas C. ;

Kellis, Manolis ;

Gelbart, William ;

Iyer, Venky N. ;

Pollard, Daniel A. ;

Sackton, Timothy B. ;

Larracuente, Amanda M. ;

Singh, Nadia D. ;

Abad, Jose P. ;

Abt, Dawn N. ;

Adryan, Boris ;

Aguade, Montserrat ;

Akashi, Hiroshi ;

Anderson, Wyatt W. ;

Aquadro, Charles F. ;

Ardell, David H. ;

Arguello, Roman ;

Artieri, Carlo G. ;

Barbash, Daniel A. ;

Barker, Daniel ;

Barsanti, Paolo ;

Batterham, Phil ;

Batzoglou, Serafim ;

Begun, Dave ;

Bhutkar, Arjun ;

Blanco, Enrico ;

Bosak, Stephanie A. ;

Bradley, Robert K. ;

Brand, Adrianne D. ;

Brent, Michael R. ;

Brooks, Angela N. ;

Brown, Randall H. ;

Butlin, Roger K. ;

Caggese, Corrado ;

Calvi, Brian R. ;

de Carvalho, A. Bernardo ;

Caspi, Anat ;

Castrezana, Sergio ;

Celniker, Susan E. ;

Chang, Jean L. ;

Chapple, Charles ;

Chatterji, Sourav ;

Chinwalla, Asif ;

Civetta, Alberto .

NATURE, 2007, 450 (7167) :203-218

[9] Stem cell transcriptome profiling via massive-scale mRNA sequencing [J].

Cloonan, Nicole ;

Forrest, Alistair R. R. ;

Kolle, Gabriel ;

Gardiner, Brooke B. A. ;

Faulkner, Geoffrey J. ;

Brown, Mellissa K. ;

Taylor, Darrin F. ;

Steptoe, Anita L. ;

Wani, Shivangi ;

Bethel, Graeme ;

Robertson, Alan J. ;

Perkins, Andrew C. ;

Bruce, Stephen J. ;

Lee, Clarence C. ;

Ranade, Swati S. ;

Peckham, Heather E. ;

Manning, Jonathan M. ;

McKernan, Kevin J. ;

Grimmond, Sean M. .

NATURE METHODS, 2008, 5 (07) :613-619

[10] Transcriptome content and dynamics at single-nucleotide resolution [J].

Cloonan, Nicole ;

Grimmond, Sean M. .

GENOME BIOLOGY, 2008, 9 (09) :234

← 1 2 3 4 5 →