publication . Article . Other literature type . 2016

flyDIVaS: A Comparative Genomics Resource for Drosophila Divergence and Selection.

Craig E. Stanley; Rob J. Kulathinal;
Open Access English
  • Published: 01 Aug 2016 Journal: G3: Genes (issn: 2160-1836, Copyright policy)
  • Publisher: Genetics Society of America
Abstract
With arguably the best finished and expertly annotated genome assembly, Drosophila melanogaster is a formidable genetics model to study all aspects of biology. Nearly a decade ago, the 12 Drosophila genomes project expanded D. melanogaster’s breadth as a comparative model through the community-development of an unprecedented genus- and genome-wide comparative resource. However, since its inception, these datasets for evolutionary inference and biological discovery have become increasingly outdated, outmoded, and inaccessible. Here, we provide an updated and upgradable comparative genomics resource of Drosophila divergence and selection, flyDIVaS, based on the la...
Subjects
free text keywords: conserved genes, rapid evolution, dN/dS, adaptation, Genetics, QH426-470, Genetics(clinical), Molecular Biology, Investigations, Orthologous Gene, Evolutionary biology, Genome, FlyBase : A Database of Drosophila Genes & Genomes, Drosophila melanogaster, biology.organism_classification, biology, Sequence assembly, Phylogenetic tree, OrthoDB, Comparative genomics
Funded by
NSF| DISSERTATION RESEARCH: Functional behavioral analysis of positively selected genes in Drosophila
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1407006
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NIH| Computational Analysis of Gene Expression Pattern Images
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002516-09
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
45 references, page 1 of 3

Allen R. C.Popat R.Diggle S. P.Brown S. P., 2014 Targeting virulence: can we make evolution-proof drugs?Nat. Rev. Microbiol.12: 300–308.24625893 [OpenAIRE] [PubMed]

Castillo-Davis C. I.Kondrashov F. A.Hartl D. L.Kulathinal R. J., 2004 The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.Genome Res.14: 802–811.15123580 [OpenAIRE] [PubMed]

Celniker S. E.Dillon L. A. L.Gerstein M. B.Gunsalus K. C.Henikoff S., 2009 Unlocking the secrets of the genome.Nature 459: 927–930.19536255 [OpenAIRE] [PubMed]

Chen Z.-X.Sturgill D.Qu J.Jiang H.Park S., 2014 Comparative validation of the D. melanogaster modENCODE transcriptome annotation.Genome Res.24: 1209–1223.24985915 [OpenAIRE] [PubMed]

Clark A. G.Lazzaro B. P., 2012 Rapid evolution of innate immune response genes, pp. 203–210 in Rapidly Evolving Genes and Genetic Systems, edited by Singh R. S.Xu J.Kulathinal R. J. Oxford University Press, Oxford. [OpenAIRE]

Clark A. G.AguadéM.Prout T.Harshman L. G.Langley C. H., 1995 Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster.Genetics 139: 189–201.7705622 [OpenAIRE] [PubMed]

Clark A. G.Eisen M. B.Smith D. R.Bergman C. M.Oliver B., 2007 Evolution of genes and genomes on the Drosophila phylogeny.Nature 450: 203–218.17994087 [PubMed]

Clark N. L.Alani E.Aquadro C. F., 2012 Evolutionary rate covariation reveals shared functionality and coexpression of genes.Genome Res.22: 714–720.22287101 [OpenAIRE] [PubMed]

Crandall K. A.Bininda-Emonds O. R. P.Mace G. M.Wayne R. K., 2000 Considering evolutionary processes in conservation biology.Trends Ecol. Evol.15: 290–295.10856956 [PubMed]

dos Santos, G., A. J. Schroeder, J. L. Goodman, V. B. Strelets, M. A. Crosby et al, 2015 FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res. 43: D690–D697.

Duret L.Mouchiroud D., 2000 Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate.Mol. Biol. Evol.17: 68–74.10666707 [OpenAIRE] [PubMed]

Edgar R. C., 2004 MUSCLE: Multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res.32: 1792–1797.15034147 [OpenAIRE] [PubMed]

Haerty W.Jagadeeshan S.Kulathinal R. J.Wong A.Ram K. R., 2007 Evolution in the fast lane: Rapidly evolving sex-related genes in Drosophila.Genetics 177: 1321–1335.18039869 [OpenAIRE] [PubMed]

Hoskins R. A.Carlson J. W.Wan K. H.Park S.Mendez I., 2015 The Release 6 reference sequence of the Drosophila melanogaster genome.Genome Res.25: 445–458.25589440 [OpenAIRE] [PubMed]

Hu T. T.Eisen M. B.Thornton K. R.Andolfatto P., 2013 A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.Genome Res.23: 89–98.22936249 [OpenAIRE] [PubMed]

45 references, page 1 of 3
Abstract
With arguably the best finished and expertly annotated genome assembly, Drosophila melanogaster is a formidable genetics model to study all aspects of biology. Nearly a decade ago, the 12 Drosophila genomes project expanded D. melanogaster’s breadth as a comparative model through the community-development of an unprecedented genus- and genome-wide comparative resource. However, since its inception, these datasets for evolutionary inference and biological discovery have become increasingly outdated, outmoded, and inaccessible. Here, we provide an updated and upgradable comparative genomics resource of Drosophila divergence and selection, flyDIVaS, based on the la...
Subjects
free text keywords: conserved genes, rapid evolution, dN/dS, adaptation, Genetics, QH426-470, Genetics(clinical), Molecular Biology, Investigations, Orthologous Gene, Evolutionary biology, Genome, FlyBase : A Database of Drosophila Genes & Genomes, Drosophila melanogaster, biology.organism_classification, biology, Sequence assembly, Phylogenetic tree, OrthoDB, Comparative genomics
Funded by
NSF| DISSERTATION RESEARCH: Functional behavioral analysis of positively selected genes in Drosophila
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1407006
  • Funding stream: Directorate for Biological Sciences | Division of Environmental Biology
,
NIH| Computational Analysis of Gene Expression Pattern Images
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01HG002516-09
  • Funding stream: NATIONAL HUMAN GENOME RESEARCH INSTITUTE
45 references, page 1 of 3

Allen R. C.Popat R.Diggle S. P.Brown S. P., 2014 Targeting virulence: can we make evolution-proof drugs?Nat. Rev. Microbiol.12: 300–308.24625893 [OpenAIRE] [PubMed]

Castillo-Davis C. I.Kondrashov F. A.Hartl D. L.Kulathinal R. J., 2004 The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.Genome Res.14: 802–811.15123580 [OpenAIRE] [PubMed]

Celniker S. E.Dillon L. A. L.Gerstein M. B.Gunsalus K. C.Henikoff S., 2009 Unlocking the secrets of the genome.Nature 459: 927–930.19536255 [OpenAIRE] [PubMed]

Chen Z.-X.Sturgill D.Qu J.Jiang H.Park S., 2014 Comparative validation of the D. melanogaster modENCODE transcriptome annotation.Genome Res.24: 1209–1223.24985915 [OpenAIRE] [PubMed]

Clark A. G.Lazzaro B. P., 2012 Rapid evolution of innate immune response genes, pp. 203–210 in Rapidly Evolving Genes and Genetic Systems, edited by Singh R. S.Xu J.Kulathinal R. J. Oxford University Press, Oxford. [OpenAIRE]

Clark A. G.AguadéM.Prout T.Harshman L. G.Langley C. H., 1995 Variation in sperm displacement and its association with accessory gland protein loci in Drosophila melanogaster.Genetics 139: 189–201.7705622 [OpenAIRE] [PubMed]

Clark A. G.Eisen M. B.Smith D. R.Bergman C. M.Oliver B., 2007 Evolution of genes and genomes on the Drosophila phylogeny.Nature 450: 203–218.17994087 [PubMed]

Clark N. L.Alani E.Aquadro C. F., 2012 Evolutionary rate covariation reveals shared functionality and coexpression of genes.Genome Res.22: 714–720.22287101 [OpenAIRE] [PubMed]

Crandall K. A.Bininda-Emonds O. R. P.Mace G. M.Wayne R. K., 2000 Considering evolutionary processes in conservation biology.Trends Ecol. Evol.15: 290–295.10856956 [PubMed]

dos Santos, G., A. J. Schroeder, J. L. Goodman, V. B. Strelets, M. A. Crosby et al, 2015 FlyBase: introduction of the Drosophila melanogaster Release 6 reference genome assembly and large-scale migration of genome annotations. Nucleic Acids Res. 43: D690–D697.

Duret L.Mouchiroud D., 2000 Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate.Mol. Biol. Evol.17: 68–74.10666707 [OpenAIRE] [PubMed]

Edgar R. C., 2004 MUSCLE: Multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res.32: 1792–1797.15034147 [OpenAIRE] [PubMed]

Haerty W.Jagadeeshan S.Kulathinal R. J.Wong A.Ram K. R., 2007 Evolution in the fast lane: Rapidly evolving sex-related genes in Drosophila.Genetics 177: 1321–1335.18039869 [OpenAIRE] [PubMed]

Hoskins R. A.Carlson J. W.Wan K. H.Park S.Mendez I., 2015 The Release 6 reference sequence of the Drosophila melanogaster genome.Genome Res.25: 445–458.25589440 [OpenAIRE] [PubMed]

Hu T. T.Eisen M. B.Thornton K. R.Andolfatto P., 2013 A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence.Genome Res.23: 89–98.22936249 [OpenAIRE] [PubMed]

45 references, page 1 of 3
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