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FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations
2014
Nucleic Acids Research
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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
2008
Heredity
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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
2017
PLoS Genetics
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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
2016
DNA Research
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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
2010
Insect molecular biology (Print)
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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
2007
PLoS Computational Biology
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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
2014
Nucleic Acids Research
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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
2013
PLoS ONE
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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
2016
Molecular biology and evolution
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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
2011
Genome Research
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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
2013
Genome Biology and Evolution
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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
2007
PLoS Biology
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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
2012
Genetics
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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
2018
Current Biology
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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
2011
Genome Biology and Evolution
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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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