Copy number increases of transposable elements and protein‐coding genes in an invasive fish of hybrid origin
暂无分享,去创建一个
[1] C. Pigott. Genetics and the Origin of Species , 1959, Nature.
[2] Dr. Susumu Ohno. Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.
[3] B. Mcclintock,et al. The significance of responses of the genome to challenge. , 1984, Science.
[4] Y. Benjamini,et al. Controlling the false discovery rate: a practical and powerful approach to multiple testing , 1995 .
[5] Loren H. Rieseberg,et al. Hybrid Origins of Plant Species , 1997 .
[6] C. Miranda,et al. Expression of a constitutive cytochrome P450 (CYP2K1) in livers of rainbow trout (Oncorhynchus mykiss) embryo and sac-fry , 1997 .
[7] R. O’Neill,et al. Undermethylation associated with retroelement activation and chromosome remodelling in an interspecific mammalian hybrid , 1998, Nature.
[8] L. Rieseberg,et al. Transgressive segregation, adaptation and speciation , 1999, Heredity.
[9] Roger Bivand,et al. Implementing functions for spatial statistical analysis using the language , 2000, J. Geogr. Syst..
[10] M. Lynch,et al. The evolutionary fate and consequences of duplicate genes. , 2000, Science.
[11] S. Henikoff,et al. The Centromere Paradox: Stable Inheritance with Rapidly Evolving DNA , 2001, Science.
[12] W. J. Kent,et al. BLAT--the BLAST-like alignment tool. , 2002, Genome research.
[13] Giovanni Parmigiani,et al. Human L1 Retrotransposition Is Associated with Genetic Instability In Vivo , 2002, Cell.
[14] P. Danielson,et al. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. , 2002, Current drug metabolism.
[15] Danielson Pb,et al. The cytochrome P450 superfamily: biochemistry, evolution and drug metabolism in humans. , 2002 .
[16] C. Pál,et al. Dosage sensitivity and the evolution of gene families in yeast , 2003, Nature.
[17] M. Cáceres,et al. The foldback-like transposon Galileo is involved in the generation of two different natural chromosomal inversions of Drosophila buzzatii. , 2003, Molecular biology and evolution.
[18] M. Labrador,et al. High transposition rates of Osvaldo, a new Drosophila buzzatii retrotransposon , 1994, Molecular and General Genetics MGG.
[19] L. Rieseberg,et al. Candidate gene polymorphisms associated with salt tolerance in wild sunflower hybrids: implications for the origin of Helianthus paradoxus, a diploid hybrid species. , 2003, The New phytologist.
[20] N. Iizuka,et al. Altered Levels of Cytochrome P450 Genes in Hepatitis B or C Virus-infected Liver Identified by Oligonucleotide Microarray. , 2004, Cancer genomics & proteomics.
[21] Juan Miguel García-Gómez,et al. BIOINFORMATICS APPLICATIONS NOTE Sequence analysis Manipulation of FASTQ data with Galaxy , 2005 .
[22] J. Jurka,et al. Repbase Update, a database of eukaryotic repetitive elements , 2005, Cytogenetic and Genome Research.
[23] A. Fontdevila. Hybrid genome evolution by transposition , 2005, Cytogenetic and Genome Research.
[24] E. Eichler,et al. Punctuated duplication seeding events during the evolution of human chromosome 2p11. , 2005, Genome research.
[25] D. Tautz,et al. An invasive lineage of sculpins, Cottus sp. (Pisces, Teleostei) in the Rhine with new habitat adaptations has originated from hybridization between old phylogeographic groups , 2005, Proceedings of the Royal Society B: Biological Sciences.
[26] R. Andrews,et al. Exon array CGH: detection of copy-number changes at the resolution of individual exons in the human genome. , 2005, American journal of human genetics.
[27] D. Tautz,et al. When invaders meet locally adapted types: rapid moulding of hybrid zones between sculpins (Cottus, Pisces) in the Rhine system , 2006, Molecular ecology.
[28] M. Batzer,et al. Emergence of primate genes by retrotransposon-mediated sequence transduction , 2006, Proceedings of the National Academy of Sciences.
[29] S. Jackson,et al. Retrotransposon accumulation and satellite amplification mediated by segmental duplication facilitate centromere expansion in rice. , 2005, Genome research.
[30] Giovanni Parmigiani,et al. Pre-processing Agilent microarray data , 2007, BMC Bioinformatics.
[31] J. Bennetzen,et al. A unified classification system for eukaryotic transposable elements , 2007, Nature Reviews Genetics.
[32] J. Mallet. Hybrid speciation , 2007, Nature.
[33] D. Hartl,et al. Genome clashes in hybrids: insights from gene expression , 2007, Heredity.
[34] R. O’Neill,et al. Genomic Instability Within Centromeres of Interspecific Marsupial Hybrids , 2007, Genetics.
[35] Sven Becker,et al. Housekeeping genes for quantitative expression studies in the three-spined stickleback Gasterosteus aculeatus , 2008, BMC Molecular Biology.
[36] M. Ungerer,et al. Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data , 2009, BMC Biology.
[37] Z. Gompert,et al. Variable patterns of introgression in two sculpin hybrid zones suggest that genomic isolation differs among populations , 2009, Molecular ecology.
[38] Beatrice Bateson,et al. William Bateson, Naturalist: Heredity and Variation in Modern Lights , 2009 .
[39] J. Hemingway,et al. Two duplicated P450 genes are associated with pyrethroid resistance in Anopheles funestus, a major malaria vector. , 2008, Genome research.
[40] P. Michalak. Epigenetic, transposon and small RNA determinants of hybrid dysfunctions , 2009, Heredity.
[41] M. Pellegrini,et al. Copy number variation influences gene expression and metabolic traits in mice. , 2009, Human molecular genetics.
[42] Richard C. Moore,et al. The genomic organization of Ty3/gypsy-like retrotransposons in Helianthus (Asteraceae) homoploid hybrid species. , 2009, American journal of botany.
[43] D. Tautz,et al. Copy number changes of CNV regions in intersubspecific crosses of the house mouse. , 2010, Molecular biology and evolution.
[44] Diethard Tautz,et al. Understanding the onset of hybrid speciation. , 2010, Trends in genetics : TIG.
[45] Sébastien Renaut,et al. Mining transcriptome sequences towards identifying adaptive single nucleotide polymorphisms in lake whitefish species pairs (Coregonus spp. Salmonidae) , 2010, Molecular ecology.
[46] F. Kondrashov,et al. The evolution of gene duplications: classifying and distinguishing between models , 2010, Nature Reviews Genetics.
[47] C. Parisod,et al. Impact of transposable elements on the organization and function of allopolyploid genomes. , 2010, The New phytologist.
[48] W. Amos. Heterozygosity and mutation rate: evidence for an interaction and its implications , 2010, BioEssays : news and reviews in molecular, cellular and developmental biology.
[49] N. Friedman,et al. Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data , 2011, Nature Biotechnology.
[50] S. Maheshwari,et al. The genetics of hybrid incompatibilities. , 2011, Annual review of genetics.
[51] A. Futschik,et al. PoPoolation: A Toolbox for Population Genetic Analysis of Next Generation Sequencing Data from Pooled Individuals , 2011, PloS one.
[52] M. Ungerer,et al. Transposable Element Proliferation and Genome Expansion Are Rare in Contemporary Sunflower Hybrid Populations Despite Widespread Transcriptional Activity of LTR Retrotransposons , 2011, Genome biology and evolution.
[53] D. Tautz,et al. Rapid formation of distinct hybrid lineages after secondary contact of two fish species (Cottus sp.) , 2011, Molecular ecology.
[54] Surong Hasi,et al. Genome sequences of wild and domestic bactrian camels , 2012, Nature Communications.
[55] F. Kondrashov. Gene duplication as a mechanism of genomic adaptation to a changing environment , 2012, Proceedings of the Royal Society B: Biological Sciences.
[56] T. Itakura,et al. Cytochrome P450 (CYP) in fish. , 2012, Environmental toxicology and pharmacology.
[57] A. Pozhitkov,et al. Transcriptome changes after genome‐wide admixture in invasive sculpins (Cottus) , 2012, Molecular ecology.
[58] Stephen J. Palmer,et al. GTF2IRD2 from the Williams–Beuren critical region encodes a mobile-element-derived fusion protein that antagonizes the action of its related family members , 2012, Journal of Cell Science.
[59] D. Joyce,et al. Gene duplication in an African cichlid adaptive radiation , 2014, BMC Genomics.
[60] M. Ungerer,et al. Transcriptional Dynamics of LTR Retrotransposons in Early Generation and Ancient Sunflower Hybrids , 2013, Genome biology and evolution.
[61] R. C. Karn,et al. The role of retrotransposons in gene family expansions: insights from the mouse Abp gene family , 2013, BMC Evolutionary Biology.
[62] U. Dieckmann,et al. Hybridization and speciation , 2013, Journal of evolutionary biology.
[63] A. Nolte,et al. The genomics of incompatibility factors and sex determination in hybridizing species of Cottus (Pisces) , 2013, Heredity.
[64] Robert A. Martienssen,et al. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond , 2013, Nature Reviews Genetics.
[65] Arndt von Haeseler,et al. NextGenMap: fast and accurate read mapping in highly polymorphic genomes , 2013, Bioinform..
[66] D. Coughlin,et al. Thermal acclimation in rainbow smelt, Osmerus mordax, leads to faster myotomal muscle contractile properties and improved swimming performance , 2013, Biology Open.
[67] Josefa González,et al. The impact of transposable elements in environmental adaptation , 2013, Molecular ecology.
[68] Yunfeng Ling,et al. Multiplexed target detection using DNA-binding dye chemistry in droplet digital PCR. , 2013, Analytical chemistry.
[69] Erich Bornberg-Bauer,et al. Genome‐wide patterns of standing genetic variation in a marine population of three‐spined sticklebacks , 2013, Molecular ecology.
[70] C. Parisod,et al. Transposable elements and microevolutionary changes in natural populations , 2013, Molecular ecology resources.
[71] Vaishali Katju,et al. Copy-number changes in evolution: rates, fitness effects and adaptive significance , 2013, Front. Genet..
[72] Helga Thorvaldsdóttir,et al. Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..
[73] A. Belyayev. Bursts of transposable elements as an evolutionary driving force , 2014, Journal of evolutionary biology.
[74] P. Andolfatto,et al. HOW COMMON IS HOMOPLOID HYBRID SPECIATION? , 2014, Evolution; international journal of organic evolution.
[75] Matthias Zytnicki,et al. Tedna: a transposable element de novo assembler , 2014, Bioinform..
[76] D. Cooper,et al. SVA retrotransposon insertion-associated deletion represents a novel mutational mechanism underlying large genomic copy number changes with non-recurrent breakpoints , 2014, Genome Biology.
[77] M. P. Guerreiro. Interspecific hybridization as a genomic stressor inducing mobilization of transposable elements in Drosophila , 2014, Mobile genetic elements.
[78] J. S. Hermansen,et al. Evidence for Mito-Nuclear and Sex-Linked Reproductive Barriers between the Hybrid Italian Sparrow and Its Parent Species , 2014, PLoS genetics.
[79] H. Quesneville,et al. PASTEC: An Automatic Transposable Element Classification Tool , 2014, PloS one.
[80] B. Langmead,et al. Lighter: fast and memory-efficient sequencing error correction without counting , 2014, Genome Biology.
[81] L. Rieseberg,et al. Genomics of homoploid hybrid speciation: diversity and transcriptional activity of long terminal repeat retrotransposons in hybrid sunflowers , 2014, Philosophical Transactions of the Royal Society B: Biological Sciences.
[82] Hanlee P. Ji,et al. Correction to High Sensitivity Detection and Quantitation of DNA Copy Number and Single Nucleotide Variants with Single Color Droplet Digital PCR , 2015, Analytical chemistry.
[83] D. Tautz,et al. A Revised Design for Microarray Experiments to Account for Experimental Noise and Uncertainty of Probe Response , 2013, PloS one.
[84] M. P. Guerreiro,et al. Changes of Osvaldo expression patterns in germline of male hybrids between the species Drosophila buzzatii and Drosophila koepferae , 2015, Molecular Genetics and Genomics.
[85] Nicholas W. Roberts,et al. Cyp27c1 Red-Shifts the Spectral Sensitivity of Photoreceptors by Converting Vitamin A1 into A2 , 2015, Current Biology.
[86] C. Parisod,et al. Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation , 2015, Proceedings of the Royal Society B: Biological Sciences.
[87] M. Tress,et al. The Evolutionary Fate of Alternatively Spliced Homologous Exons after Gene Duplication , 2015, Genome biology and evolution.
[88] G. Fain. Phototransduction: Making the Chromophore to See Through the Murk , 2015, Current Biology.
[89] Matthew E. Ritchie,et al. limma powers differential expression analyses for RNA-sequencing and microarray studies , 2015, Nucleic acids research.
[90] C. Parisod,et al. Differential introgression and reorganization of retrotransposons in hybrid zones between wild wheats , 2016, Molecular ecology.
[91] Robert D. Finn,et al. The Pfam protein families database: towards a more sustainable future , 2015, Nucleic Acids Res..
[92] Srikanth Gottipati,et al. Evidence for the fixation of gene duplications by positive selection in Drosophila , 2016, Genome research.
[93] L. Hurst,et al. Mutation rate analysis via parent–progeny sequencing of the perennial peach. I. A low rate in woody perennials and a higher mutagenicity in hybrids , 2016, Proceedings of the Royal Society B: Biological Sciences.
[94] C. Feschotte,et al. Regulatory evolution of innate immunity through co-option of endogenous retroviruses , 2016, Science.