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FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations

G. dos Santos, A. J. Schroeder, J. L. Goodman, V. B. Strelets, M. A. Crosby, J. Thurmond, D. B. Emmert, W. M. Gelbart
2014 Nucleic Acids Research  
In this report, we describe the attributes of the new Release 6 reference genome assembly, the migration of FlyBase genome annotations to this new assembly, how genome features on this new assembly can  ...  Release 6, the latest reference genome assembly of the fruit fly Drosophila melanogaster, was released by the Berkeley Drosophila Genome Project in 2014; it replaces their previous Release 5 genome assembly  ...  ACKNOWLEDGEMENTS We would like to thank the BDGP for advance access to the Release 6 genome assembly and associated metadata. We  ... 
doi:10.1093/nar/gku1099 pmid:25398896 pmcid:PMC4383921 fatcat:yp2eeb5ay5ejzirljctnv7wysm

Genome size diversity in the family Drosophilidae

T R Gregory, J S Johnston
2008 Heredity  
Another benefit of using Drosophila as a comparative genomic model is that an active community, working via the Flybase interface, has already greatly assisted the annotation of D. melanogaster and D.  ...  As the 1/30 th scale model for annotation of the human or mouse genome, Drosophila provides exceptional opportunities for biological interpretation of genomic diversity.  ... 
doi:10.1038/hdy.2008.49 pmid:18523443 fatcat:k7ykpxzpenc45gpkifmtwvybom

Genomics of parallel adaptation at two timescales in Drosophila

Li Zhao, David J. Begun, Luciano Matzkin
2017 PLoS Genetics  
Drosophila melanogaster is a key model system for population and evolutionary genomics.  ...  D. hydei, a member of the repleta group of Drosophila, is similar to D. melanogaster, in that it too appears to be a recently cosmopolitan species and recent colonizer of high latitude environments.  ...  Lee of Lawrence Berkeley National Laboratory for generously providing the pairwise D. melanogaster-D. simulans MK test results and estimates of synonymous and non-synonymous π for D. melanogaster.  ... 
doi:10.1371/journal.pgen.1007016 pmid:28968391 pmcid:PMC5638604 fatcat:pcqd7l6cmvaylhcku622hurcnm

Ultra-deep sequencing of ribosome-associated poly-adenylated RNA in earlyDrosophilaembryos reveals hundreds of conserved translated sORFs

Hongmei Li, Chuansheng Hu, Ling Bai, Hua Li, Mingfa Li, Xiaodong Zhao, Daniel M. Czajkowsky, Zhifeng Shao
2016 DNA Research  
These results thus provide the first comprehensive annotation of the sORFs present during early Drosophila embryogenesis, a necessary basis for a detailed delineation of their function in embryogenesis  ...  There is growing recognition that small open reading frames (sORFs) encoding peptides shorter than 100 amino acids are an important class of functional elements in the eukaryotic genome, with several already  ...  Acknowledgements The authors thank Professor Nan Liu from the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, for providing the S2Rþ cell line and vectors.  ... 
doi:10.1093/dnares/dsw040 pmid:27559081 pmcid:PMC5144680 fatcat:rvmcocchvvhmhkjpptikjibxdq

The pea aphid phylome: a complete catalogue of evolutionary histories and arthropod orthology and paralogy relationships for Acyrthosiphon pisum genes

J. Huerta-Cepas, M. Marcet-Houben, M. Pignatelli, A. Moya, T. Gabaldón
2010 Insect molecular biology (Print)  
with Drosophila melanogaster annotated genes.  ...  Within the context of the sequencing of the genome of the pea aphid, Acyrthosiphon pisum, we undertook a phylogenetic analysis for every protein of this species.  ...  Acknowledgements The authors are grateful to the International Pediculus humanus and Nasonia vitripenis genome sequencing consortia for providing the data before publication.  ... 
doi:10.1111/j.1365-2583.2009.00947.x pmid:20482636 fatcat:3dd5273g6zc2tmpuktr3arhe2m

Prediction of Gene Expression in Embryonic Structures of Drosophila melanogaster

Anastasia A. Samsonova, Mahesan Niranjan, Steven Russell, Alvis Brazma
2007 PLoS Computational Biology  
The use of high-throughput approaches, such as large-scale in situ hybridisation and genome-wide expression profiling via DNA microarrays, is beginning to provide insights into the complexities of development  ...  The reliability of our predictions is confirmed by literature-derived annotations in FlyBase, by overrepresentation of Gene Ontology biological process annotations, and, in a selected set, by detailed  ...  MN is grateful to the EBI for hosting his study leave. Author contributions. AAS and MN conceived and designed the experiments and performed the experiments. AAS, SR, and AB analyzed the data.  ... 
doi:10.1371/journal.pcbi.0030144 pmid:17658945 pmcid:PMC1924873 fatcat:lcqman5sbfgvro7yqu4rv324sy

The UCSC Genome Browser database: 2015 update

Kate R. Rosenbloom, Joel Armstrong, Galt P. Barber, Jonathan Casper, Hiram Clawson, Mark Diekhans, Timothy R. Dreszer, Pauline A. Fujita, Luvina Guruvadoo, Maximilian Haeussler, Rachel A. Harte, Steve Heitner (+17 others)
2014 Nucleic Acids Research  
large database of genome assemblies and their associated annotations.  ...  Some release highlights of this year include new and updated genome browsers for various assemblies, including bonobo and zebrafish; new gene annotation sets; improvements to track and assembly hub support  ...  group of system administrators who keep the Genome Browser running.  ... 
doi:10.1093/nar/gku1177 pmid:25428374 pmcid:PMC4383971 fatcat:sahorqoiejam7maduvqkqrh4de

Variation of Gene Expression Associated with Colonisation of an Anthropized Environment: Comparison between African and European Populations of Drosophila simulans

François Wurmser, Tristan Mary-Huard, Jean-Jacques Daudin, Dominique Joly, Catherine Montchamp-Moreau, Richard Cordaux
2013 PLoS ONE  
The increasing amount of data produced by comparative population genomics and transcriptomics should permit the identification of additional genes associated with functional divergence among those differentially  ...  In this study, we use massively parallel sequencing of 39 cDNAs obtained from large samples of adult males, to compare a population of Drosophila simulans from a natural reserve within its ancestral range  ...  We are grateful to the INRA of Gotheron for welcoming us on their fields. We also thank GATC, especially Benjamin Moingeon and Dr Yadhu Kumar for the sequencing and helpful discussions.  ... 
doi:10.1371/journal.pone.0079750 pmid:24260296 pmcid:PMC3832527 fatcat:q2wzd4j3mvcijhzja64hmwlhsu

Parallel Evolution of Copy-Number Variation across Continents inDrosophila melanogaster

Daniel R. Schrider, Matthew W. Hahn, David J. Begun
2016 Molecular biology and evolution  
In Drosophila melanogaster, the latitudinal clines across the eastern coasts of Australia and North America appear to be examples of this type of selection, with recent studies showing that a substantial  ...  portion of the D. melanogaster genome exhibits allele frequency differentiation with respect to latitude on both continents.  ...  For D. simulans, we used the locations of orthologs to FlyBase release 33 genes found by Hu et al. (2013) and again used the FlyBase GO annotations.  ... 
doi:10.1093/molbev/msw014 pmid:26809315 pmcid:PMC4909135 fatcat:mqf7jq3sgbcddbk4iwyi4rjvhe

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

D. R. Schrider, K. Stevens, C. M. Cardeno, C. H. Langley, M. W. Hahn
2011 Genome Research  
Here, we examine 37 Illuminasequenced North American Drosophila melanogaster inbred lines and present the first ever data set and analysis of polymorphic retrogenes in Drosophila.  ...  We show that these polymorphisms are all in fact deletions rather than intron gain events present in the reference genome.  ...  Kern for conducting the frequency spectrum analysis and also thank D. Begun, A. Tucker, and K. Pollard for very helpful suggestions.  ... 
doi:10.1101/gr.116434.110 pmid:22135405 pmcid:PMC3227099 fatcat:xmbjgwxjobbe5pqklzyvzqsarq

Linking Genomics and Ecology to Investigate the Complex Evolution of an Invasive Drosophila Pest

Lino Ometto, Alessandro Cestaro, Sukanya Ramasamy, Alberto Grassi, Santosh Revadi, Stefanos Siozios, Marco Moretto, Paolo Fontana, Claudio Varotto, Davide Pisani, Teun Dekker, Nicola Wrobel (+6 others)
2013 Genome Biology and Evolution  
Although the D. suzukii genome is comparable in size and repeat content to other Drosophila species, it has the lowest nucleotide substitution rate among the species analyzed in this study.  ...  Using nuclear and mitochondrial phylogenetic analyses, we confirm its Asian origin and reveal a surprising sister relationship between the eugracilis and the melanogaster subgroups.  ...  Acknowledgments The authors acknowledge the Baylor College of Medicine Human Genome Sequencing Center and the NHGRI for prepublication access to their data and staff of the GenePool for their support.  ... 
doi:10.1093/gbe/evt034 pmid:23501831 pmcid:PMC3641628 fatcat:scqoeyzekvgfld2koxaa7bcvdu

Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans

David J Begun, Alisha K Holloway, Kristian Stevens, LaDeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers (+2 others)
2007 PLoS Biology  
Here we present a population genetic analysis of Drosophila simulans based on whole-genome shotgun sequencing of multiple inbred lines and comparison of the resulting data to genome assemblies of the closely  ...  We used this approach to carry out whole-genome analysis of polymorphism and divergence in Drosophila simulans, a close relative of the model system, D. melanogaster.  ...  Estimates of Polymorphism, Divergence, and Counts of Polymorphic and Fixed Sites for CDS Found at doi: 10 Population Genomics of D. simulans melanogaster alignment was by CND and LP.  ... 
doi:10.1371/journal.pbio.0050310 pmid:17988176 pmcid:PMC2062478 fatcat:cs7finhyyrfpxpoqtxniwpivja

Genomic Variation in Natural Populations of Drosophila melanogaster

C. H. Langley, K. Stevens, C. Cardeno, Y. C. G. Lee, D. R. Schrider, J. E. Pool, S. A. Langley, C. Suarez, R. B. Corbett-Detig, B. Kolaczkowski, S. Fang, P. M. Nista (+6 others)
2012 Genetics  
Because this short read resequencing technology is ineffective in repetitive genomic regions this study focuses only on the five large euchromatic "chromosomes" of the melanogaster reference sequence (  ...  Assembly and Quality Calibration The genome sequences were assembled using the MAQ program described in (LI et al. 2008) .  ...  ACKNOWLEDGEMENTS Funding: YSS: NIH grants R00-GM080099 and R01-GM094402. ADK: the Neukom Institute and Dartmouth College. CHL: NIH grant HG02942.  ... 
doi:10.1534/genetics.112.142018 pmid:22673804 pmcid:PMC3454882 fatcat:ds5p3nq2ujdtznwie7xvs4zhzm

Non-coding RNA Expression, Function, and Variation during Drosophila Embryogenesis

Ignacio E. Schor, Giovanni Bussotti, Matilda Maleš, Mattia Forneris, Rebecca R. Viales, Anton J. Enright, Eileen E.M. Furlong
2018 Current Biology  
The FlyBase reference annotations version r5.55 were used to guide the assemblies. In parallel, Trinity [69] release 2014-07-17 was used to assemble transcript isoforms de novo.  ...  Assembled transcripts were projected onto the Drosophila melanogaster genome dm3 with the splice mapper GMAP [70] version 2013-03-31.  ...  CONTACT FOR REAGENT AND RESOURCE SHARING Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Eileen E.M.  ... 
doi:10.1016/j.cub.2018.09.026 fatcat:h24sqfnibrg2dn4hvlzpufdqse

Widespread Polymorphism in the Positions of Stop Codons in Drosophila melanogaster

Yuh Chwen G. Lee, Josephine A. Reinhardt
2011 Genome Biology and Evolution  
Here, we use Drosophila melanogaster population genomic data combined with between species divergence information to understand the evolutionary forces that generate and maintain polymorphisms causing  ...  SCPs likely have an important role in the evolution of these genes.  ...  Acknowledgments We thank DPGP for providing access to the Drosophila melanogaster and Drosophila simulans genome sequences and multispecies genomic alignment.  ... 
doi:10.1093/gbe/evr113 pmid:22051795 pmcid:PMC3342867 fatcat:tta55ldwhfegtjftuqzjqxl4qm
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