Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Alexander Stark,Michael F. Lin,Pouya Kheradpour,Jakob Skou Pedersen,Jakob Skou Pedersen,Leopold Parts,Leopold Parts,Joseph W. Carlson,Madeline A. Crosby,Matthew D. Rasmussen,Sushmita Roy,Ameya N. Deoras,J. Graham Ruby,Julius Brennecke,Emily Hodges,Angie S. Hinrichs,Anat Caspi,Benedict Paten,Benedict Paten,Benedict Paten,Seung-Won Park,Mira V. Han,Morgan L. Maeder,Benjamin J. Polansky,Bryanne E. Robson,Stein Aerts,Jacques van Helden,Bassem A. Hassan,Donald G. Gilbert,Deborah Eastman,Michael D. Rice,Michael P. Weir,Matthew W. Hahn,Yongkyu Park,Colin N. Dewey,Lior Pachter,W. James Kent,David Haussler,Eric C. Lai,David P. Bartel,Gregory J. Hannon,Thomas C. Kaufman,Michael B. Eisen,Michael B. Eisen,Andrew G. Clark,Douglas Smith,Susan E. Celniker,William M. Gelbart,Manolis Kellis +48 more
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This work uses the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly, and identifies several classes of pre- and post-transcriptional regulatory motifs, and predicts individual motif instances with high confidence.Abstract:
Sequencing of multiple related species followed by comparative genomics analysis constitutes a powerful approach for the systematic understanding of any genome. Here, we use the genomes of 12 Drosophila species for the de novo discovery of functional elements in the fly. Each type of functional element shows characteristic patterns of change, or 'evolutionary signatures', dictated by its precise selective constraints. Such signatures enable recognition of new protein-coding genes and exons, spurious and incorrect gene annotations, and numerous unusual gene structures, including abundant stop-codon readthrough. Similarly, we predict non-protein-coding RNA genes and structures, and new microRNA (miRNA) genes. We provide evidence of miRNA processing and functionality from both hairpin arms and both DNA strands. We identify several classes of pre- and post-transcriptional regulatory motifs, and predict individual motif instances with high confidence. We also study how discovery power scales with the divergence and number of species compared, and we provide general guidelines for comparative studies.read more
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MicroRNAs: Target Recognition and Regulatory Functions
TL;DR: The current understanding of miRNA target recognition in animals is outlined and the widespread impact of miRNAs on both the expression and evolution of protein-coding genes is discussed.
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Evolution of genes and genomes on the Drosophila phylogeny.
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Delehaunty,Chuong B. Do,Heather Ebling,Kevin A. Edwards,Thomas H. Eickbush,Jay D. Evans,Alan Filipski,Sven Findeiß,Sven Findeiß,Eva Freyhult,Lucinda Fulton,Robert S. Fulton,Ana Cristina Lauer Garcia,Anastasia Gardiner,David A. Garfield,Barry E. Garvin,Greg Gibson,Don Gilbert,Sante Gnerre,Jennifer Godfrey,Robert T. Good,Valer Gotea,Brenton Gravely,Anthony J. Greenberg,Sam Griffiths-Jones,Sam Griffiths-Jones,Samuel R. Gross,Roderic Guigó,Erik Gustafson,Wilfried Haerty,Matthew W. Hahn,Daniel L. Halligan,Aaron L. Halpern,Gillian M. Halter,Mira V. Han,Andreas Heger,LaDeana W. Hillier,Angie S. Hinrichs,Ian Holmes,Roger A. Hoskins,Melissa J. Hubisz,Dan Hultmark,Melanie A. Huntley,David B. Jaffe,Santosh Jagadeeshan,William R. Jeck,Justin Johnson,Corbin D. Jones,William C. Jordan,Gary H. Karpen,Gary H. Karpen,Eiko Kataoka,Peter D. Keightley,Pouya Kheradpour,Ewen F. Kirkness,Leonardo Koerich,Karsten Kristiansen,Dave Kudrna,Rob J. Kulathinal,Sudhir Kumar,Roberta Kwok,Eric S. Lander,Charles H. 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TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
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