The Gypsy Database (GyDB) of mobile genetic elements: release 2.0

This article introduces the second release of the Gypsy Database of Mobile Genetic Elements (GyDB 2.0): a research project devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (per lineage and protein domain). The Gypsy Database (GyDB) is a long-term project that is continuously progressing, and that owing to the high molecular diversity of mobile elements requires to be completed in several stages. GyDB 2.0 has been powered with a wiki to allow other researchers participate in the project. The current database stage and scope are long terminal repeats (LTR) retroelements and relatives. GyDB 2.0 is an update based on the analysis of Ty3/Gypsy, Retroviridae, Ty1/Copia and Bel/Pao LTR retroelements and the Caulimoviridae pararetroviruses of plants. Among other features, in terms of the aforementioned topics, this update adds: (i) a variety of descriptions and reviews distributed in multiple web pages; (ii) protein-based phylogenies, where phylogenetic levels are assigned to distinct classified elements; (iii) a collection of multiple alignments, lineage-specific hidden Markov models and consensus sequences, called GyDB collection; (iv) updated RefSeq databases and BLAST and HMM servers to facilitate sequence characterization of new LTR retroelement and caulimovirus queries; and (v) a bibliographic server. GyDB 2.0 is available at http://gydb.org.

[1]  Elliot J. Lefkowitz,et al.  Virus taxonomy: classification and nomenclature of viruses , 2012 .

[2]  L. Poggio,et al.  Genomic screening in dioecious “yerba mate” tree (Ilex paraguariensis A. St. Hill., Aquifoliaceae) through representational difference analysis , 2010, Genetica.

[3]  G. K. Davis,et al.  Genome Sequence of the Pea Aphid Acyrthosiphon pisum , 2010, PLoS biology.

[4]  Neil D. Rawlings,et al.  MEROPS: the peptidase database , 2009, Nucleic Acids Res..

[5]  M. Kimmel,et al.  Conflict of interest statement. None declared. , 2010 .

[6]  C. Bowler,et al.  Potential impact of stress activated retrotransposons on genome evolution in a marine diatom , 2009, BMC Genomics.

[7]  Claudia M. A. Carareto,et al.  Multiple invasions of Gypsy and Micropia retroelements in genus Zaprionus and melanogaster subgroup of the genus Drosophila , 2009, BMC Evolutionary Biology.

[8]  S. Jackson,et al.  A lineage-specific centromere retrotransposon in Oryza brachyantha. , 2009, The Plant journal : for cell and molecular biology.

[9]  A. Moya,et al.  Network dynamics of eukaryotic LTR retroelements beyond phylogenetic trees , 2009, Biology Direct.

[10]  N. Okada,et al.  The evolution of two partner LINE/SINE families and a full-length chromodomain-containing Ty3/Gypsy LTR element in the first reptilian genome of Anolis carolinensis. , 2009, Gene.

[11]  Andrés Moya,et al.  Bioinformatic flowchart and database to investigate the origins and diversity of Clan AA peptidases , 2009, Biology Direct.

[12]  O. Pisarenko,et al.  Novel clades of chromodomain-containing Gypsy LTR retrotransposons from mosses (Bryophyta). , 2008, The Plant journal : for cell and molecular biology.

[13]  Jonathan B. Clark,et al.  Gypsy endogenous retrovirus maintains potential infectivity in several species of Drosophilids , 2008, BMC Evolutionary Biology.

[14]  M. Rhyu,et al.  PwRn1, a novel Ty3/gypsy-like retrotransposon of Paragonimus westermani: molecular characters and its differentially preserved mobile potential according to host chromosomal polyploidy , 2008, BMC Genomics.

[15]  A. Moya,et al.  Relationships of gag-pol diversity between Ty3/Gypsy and Retroviridae LTR retroelements and the three kings hypothesis , 2008, BMC Evolutionary Biology.

[16]  E. Douzery,et al.  Taxonomy, molecular phylogeny and evolution of plant reverse transcribing viruses (family Caulimoviridae) inferred from full-length genome and reverse transcriptase sequences , 2008, Archives of Virology.

[17]  Jan Gründemann,et al.  Elevated α-synuclein mRNA levels in individual UV-laser-microdissected dopaminergic substantia nigra neurons in idiopathic Parkinson's disease , 2008, Nucleic acids research.

[18]  A. Moya,et al.  The Gypsy Database (GyDB) of mobile genetic elements , 2007, Nucleic Acids Res..

[19]  Antonio Marco,et al.  How Athila retrotransposons survive in the Arabidopsis genome , 2008, BMC Genomics.

[20]  M. Meselson,et al.  A deep-branching clade of retrovirus-like retrotransposons in bdelloid rotifers. , 2007, Gene.

[21]  J. Brosius,et al.  Modern genomes with retro-look: retrotransposed elements, retroposition and the origin of new genes. , 2007, Genome dynamics.

[22]  J. Jurka,et al.  Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.

[23]  Casey M. Bergman,et al.  Combined Evidence Annotation of Transposable Elements in Genome Sequences , 2005, PLoS Comput. Biol..

[24]  M. Tristem,et al.  Evolution and Distribution of Class II-Related Endogenous Retroviruses , 2005, Journal of Virology.

[25]  J. Volff,et al.  Retroelement dynamics and a novel type of chordate retrovirus-like element in the miniature genome of the tunicate Oikopleura dioica. , 2004, Molecular biology and evolution.

[26]  D. Kordis,et al.  Evolutionary genomics of chromoviruses in eukaryotes. , 2004, Molecular biology and evolution.

[27]  P. Herron,et al.  Mobile DNA II , 2004, Heredity.

[28]  H. Kazazian.  Mobile Elements: Drivers of Genome Evolution , 2004, Science.

[29]  J. Chermann,et al.  Isolation of a T-lymphotropic retrovirus from a patient at risk for acquired immune deficiency syndrome (AIDS). 1983. , 2004, Revista de investigacion clinica; organo del Hospital de Enfermedades de la Nutricion.

[30]  M. Tristem,et al.  The Evolution, Distribution and Diversity of Endogenous Retroviruses , 2003, Virus Genes.

[31]  Claude Bazin,et al.  Is the evolution of transposable elements modular? , 2004, Genetica.

[32]  Shoshana J. Wodak,et al.  ACLAME: A CLAssification of Mobile genetic Elements , 2004, Nucleic Acids Res..

[33]  K. Crandall,et al.  The causes and consequences of HIV evolution , 2004, Nature Reviews Genetics.

[34]  M. Lynch,et al.  The Origins of Genome Complexity , 2003, Science.

[35]  T. Chowdhury,et al.  Severe Refractory Hypercalcaemia in HTLV-1 Infection , 2003, Journal of the Royal Society of Medicine.

[36]  Jean-Michel Hatt,et al.  Identification and Characterization of Two Closely Related Unclassifiable Endogenous Retroviruses in Pythons ( Python molurus and Python curtus ) , 2022 .

[37]  R. Poulter,et al.  A group of deuterostome Ty3/gypsy-like retrotransposons with Ty1/copia-like pol-domain orders , 2002, Molecular Genetics and Genomics.

[38]  T. Eickbush,et al.  Origins and Evolution of Retrotransposons , 2002 .

[39]  Alan M. Lambowitz,et al.  Mobile DNA III , 2002 .

[40]  David A Wright,et al.  Athila4 of Arabidopsis and Calypso of soybean define a lineage of endogenous plant retroviruses. , 2002, Genome research.

[41]  C. Lloréns,et al.  A mammalian gene evolved from the integrase domain of an LTR retrotransposon. , 2001, Molecular biology and evolution.

[42]  M. Rhyu,et al.  CsRn1, a novel active retrotransposon in a parasitic trematode, Clonorchis sinensis, discloses a new phylogenetic clade of Ty3/gypsy-like LTR retrotransposons. , 2001, Molecular biology and evolution.

[43]  T. Eickbush,et al.  Phylogenetic analysis of ribonuclease H domains suggests a late, chimeric origin of LTR retrotransposable elements and retroviruses. , 2001, Genome research.

[44]  International Human Genome Sequencing Consortium.  Initial sequencing and analysis of the human genome , 2001, Nature.

[45]  C. Lloréns,et al.  Ty3/Gypsy retrotransposons: description of new Arabidopsis thaliana elements and evolutionary perspectives derived from comparative genomic data. , 2000, Molecular biology and evolution.

[46]  M. Palmarini,et al.  An accessory open reading frame (orf-x) of jaagsiekte sheep retrovirus is conserved between different virus isolates. , 2000, Virus research.

[47]  I. K. Jordan,et al.  Evidence for the recent horizontal transfer of long terminal repeat retrotransposon. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[48]  A. Flavell.  Long terminal repeat retrotransposons jump between species. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[49]  N. Bowen,et al.  Genomic analysis of Caenorhabditis elegans reveals ancient families of retroviral-like elements. , 1999, Genome research.

[50]  M. Labrador,et al.  The retrotransposon Osvaldo from Drosophila buzzatii displays all structural features of a functional retrovirus. , 1999, Molecular biology and evolution.

[51]  J. Bai,et al.  Sequence comparison of JSRV with endogenous proviruses: envelope genotypes and a novel ORF with similarity to a G-protein-coupled receptor. , 1999, Virology.

[52]  T. Eickbush,et al.  Modular Evolution of the Integrase Domain in the Ty3/Gypsy Class of LTR Retrotransposons , 1999, Journal of Virology.

[53]  R. Hull,et al.  Classification of reverse transcribing elements: a discussion document , 1999, Archives of Virology.

[54]  D. Voytas,et al.  Potential retroviruses in plants: Tat1 is related to a group of Arabidopsis thaliana Ty3/gypsy retrotransposons that encode envelope-like proteins. , 1998, Genetics.

[55]  M. Schilthuizen,et al.  Selfish genetic elements and speciation , 1998, Heredity.

[56]  Sean R. Eddy,et al.  Profile hidden Markov models , 1998, Bioinform..

[57]  David L. Wheeler,et al.  GenBank , 2015, Nucleic Acids Res..

[58]  J. Thompson,et al.  The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. , 1997, Nucleic acids research.

[59]  Thomas L. Madden,et al.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. , 1997, Nucleic acids research.

[60]  S. Wessler,et al.  A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[61]  S. Wessler,et al.  LTR-retrotransposons and MITEs: important players in the evolution of plant genomes. , 1995, Current opinion in genetics & development.

[62]  R. Britten,et al.  Active gypsy/Ty3 retrotransposons or retroviruses in Caenorhabditis elegans. , 1995, Proceedings of the National Academy of Sciences of the United States of America.

[63]  N. Rawlings,et al.  Families of aspartic peptidases, and those of unknown catalytic mechanism. , 1995, Methods in enzymology.

[64]  E. Koonin,et al.  The chromo superfamily: new members, duplication of the chromo domain and possible role in delivering transcription regulators to chromatin. , 1995, Nucleic acids research.

[65]  J. Maniloff,et al.  Virus taxonomy : eighth report of the International Committee on Taxonomy of Viruses , 2005 .

[66]  J. Boeke,et al.  An env-like protein encoded by a Drosophila retroelement: evidence that gypsy is an infectious retrovirus. , 1994, Genes & development.

[67]  A. Pélisson,et al.  Retroviruses in invertebrates: the gypsy retrotransposon is apparently an infectious retrovirus of Drosophila melanogaster. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[68]  D. Mager,et al.  Endogenous Human Retroviruses , 1994 .

[69]  P. Luciw,et al.  Distinct subsets of retroviruses encode dUTPase , 1992, Journal of virology.

[70]  K. Mizuuchi,et al.  Transpositional recombination: mechanistic insights from studies of mu and other elements. , 1992, Annual review of biochemistry.

[71]  E. Koonin,et al.  Diverse groups of plant RNA and DNA viruses share related movement proteins that may possess chaperone-like activity. , 1991, The Journal of general virology.

[72]  T. Eickbush,et al.  Origin and evolution of retroelements based upon their reverse transcriptase sequences. , 1990, The EMBO journal.

[73]  R. Weiss,et al.  Receptor interference groups of 20 retroviruses plating on human cells. , 1990, Virology.

[74]  H. Temin.  Reverse transcriptases. Retrons in bacteria. , 1989, Nature.

[75]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[76]  S. Wain-Hobson,et al.  Nucleotide sequence of Mason-Pfizer monkey virus: An immunosuppressive D-type retrovirus , 1986, Cell.

[77]  J. Levy,et al.  Recovery of AIDS-associated retroviruses from patients with AIDS or AIDS-related conditions and from clinically healthy individuals. , 1985, The Journal of infectious diseases.

[78]  Stephen M. Mount,et al.  Complete nucleotide sequence of the Drosophila transposable element copia: homology between copia and retroviral proteins , 1985, Molecular and cellular biology.

[79]  P. Farabaugh,et al.  Nucleotide sequence of a yeast Ty element: evidence for an unusual mechanism of gene expression. , 1985, Proceedings of the National Academy of Sciences of the United States of America.

[80]  Tom Blundell,et al.  The active site of aspartic proteinases , 1991, FEBS letters.

[81]  Y. Matsuo,et al.  Identification of the coding sequence for a reverse transcriptase-like enzyme in a transposable genetic element in Drosophila melanogaster , 1984, Nature.

[82]  B. Haynes,et al.  Frequent detection and isolation of cytopathic retroviruses (HTLV-III) from patients with AIDS and at risk for AIDS. , 1984, Science.

[83]  M. Yoshida,et al.  Isolation and characterization of retrovirus from cell lines of human adult T-cell leukemia and its implication in the disease. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[84]  Fred R. McMorris,et al.  Consensusn-trees , 1981 .

[85]  John D. Minna,et al.  Detection and isolation of type C retrovirus particles from fresh and cultured lymphocytes of a patient with cutaneous T-cell lymphoma , 1980, Proceedings of the National Academy of Sciences.

[86]  E. Hunter,et al.  Fusion of normal primate cells: a common biological property of the D-type retroviruses. , 1980, Virology.

[87]  J. Farris,et al.  Quantitative Phyletics and the Evolution of Anurans , 1969 .

[88]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[89]  B. Mcclintock.  Mutable Loci in Maize , 1951 .