The Genomic Impact of Gene Retrocopies: What Have We Learned from Comparative Genomics, Population Genomics, and Transcriptomic Analyses?

Comparative genomic analysis of retrogene repertoire in two green algae Volvox carteri and Chlamydomonas reinhardtii

(2016) Marcin Jąkalski et al.   Biology Direct

Human adaptation and evolution by segmental duplication

(2016) Megan Y Dennis et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

LTR-mediated retroposition as a mechanism of RNA-based duplication in metazoans

(2016) Shengjun Tan et al.   GENOME RESEARCH

The life history of retrocopies illuminates the evolution of new mammalian genes

(2016) Francesco Nicola Carelli et al.   GENOME RESEARCH

Evidence for the fixation of gene duplications by positive selection inDrosophila

(2016) Margarida Cardoso-Moreira et al.   GENOME RESEARCH

Expression of the human isoform of glutamate dehydrogenase, hGDH2, augments TCA cycle capacity and oxidative metabolism of glutamate during glucose deprivation in astrocytes

(2016) Jakob D. Nissen et al.   GLIA

Mice carrying a humanGLUD2gene recapitulate aspects of human transcriptome and metabolome development

(2016) Qian Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary interplay between sister cytochrome P450 genes shapes plasticity in plant metabolism

(2016) Zhenhua Liu et al.   Nature Communications

LINE-1-like retrotransposons contribute to RNA-based gene duplication in dicots

(2016) Zhenglin Zhu et al.   Scientific Reports

Sex Chromosome-wide Transcriptional Suppression and Compensatory Cis-Regulatory Evolution Mediate Gene Expression in the Drosophila Male Germline

(2016) Emily L. Landeen et al.   PLOS BIOLOGY

Identification and analysis of retrogenes in the East Asian nematode Caenorhabditis sp. 5 genome

(2015) Kun Zhou et al.   GENOME

A Genome-Wide Landscape of Retrocopies in Primate Genomes

(2015) Fábio C.P. Navarro et al.   Genome Biology and Evolution

Potential Mechanisms for Cancer Resistance in Elephants and Comparative Cellular Response to DNA Damage in Humans

(2015) Lisa M. Abegglen et al.   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

The Specific Requirements for CR1 Retrotransposition Explain the Scarcity of Retrogenes in Birds

(2015) Alexander Suh   JOURNAL OF MOLECULAR EVOLUTION

The “Life Histories” of Genes

(2015) Esther Betrán   JOURNAL OF MOLECULAR EVOLUTION

Correlated expression of retrocopies and parental genes in zebrafish

(2015) Zaixuan Zhong et al.   MOLECULAR GENETICS AND GENOMICS

A copy number variation map of the human genome

(2015) Mehdi Zarrei et al.   NATURE REVIEWS GENETICS

Genetic and epigenetic architecture of sex-biased expression in the jewel waspsNasonia vitripennisandgiraulti

(2015) Xu Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sex chromosome-to-autosome transposition events counter Y-chromosome gene loss in mammals

(2015) Jennifer F Hughes et al.   GENOME BIOLOGY

Diversity through duplication: Whole-genome sequencing reveals novel gene retrocopies in the human population

(2014) Sandra R. Richardson et al.   BIOESSAYS

Retrotransposons and pseudogenes regulate mRNAs and lncRNAs via the piRNA pathway in the germline

(2014) Toshiaki Watanabe et al.   GENOME RESEARCH

Relocation Facilitates the Acquisition of Short Cis-Regulatory Regions that Drive the Expression of Retrogenes during Spermatogenesis in Drosophila

(2014) Mehran Sorourian et al.   MOLECULAR BIOLOGY AND EVOLUTION

RetrogeneDB—A Database of Animal Retrogenes

(2014) Michał Kabza et al.   MOLECULAR BIOLOGY AND EVOLUTION

The common marmoset genome provides insight into primate biology and evolution

(2014) Kim C Worley et al.   NATURE GENETICS

Pollen-Specific Activation of Arabidopsis Retrogenes Is Associated with Global Transcriptional Reprogramming

(2014) A. Abdelsamad et al.   PLANT CELL

Evolution of Gene Structural Complexity: An Alternative-Splicing-Based Model Accounts for Intron-Containing Retrogenes

(2014) C. Zhang et al.   PLANT PHYSIOLOGY

Origin of Spliceosomal Introns and Alternative Splicing

(2014) M. Irimia et al.   Cold Spring Harbor Perspectives in Biology

RCPedia: a database of retrocopied genes

(2013) Fábio C. P. Navarro et al.   BIOINFORMATICS

midlife crisis encodes a conserved zinc-finger protein required to maintain neuronal differentiation in Drosophila

(2013) T. D. Carney et al.   DEVELOPMENT

The role of mRNA-based duplication in the evolution of the primate genome

(2013) Qu Zhang   FEBS LETTERS

Analysis of variable retroduplications in human populations suggests coupling of retrotransposition to cell division

(2013) A. Abyzov et al.   GENOME RESEARCH

Accelerated Evolution after Gene Duplication: A Time-Dependent Process Affecting Just One Copy

(2013) Cinta Pegueroles et al.   MOLECULAR BIOLOGY AND EVOLUTION

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

The RNA Export Factor, Nxt1, Is Required for Tissue Specific Transcriptional Regulation

(2013) Simona Caporilli et al.   PLoS Genetics

Gene Copy-Number Polymorphism Caused by Retrotransposition in Humans

(2013) Daniel R. Schrider et al.   PLoS Genetics

Retrotransposition of gene transcripts leads to structural variation in mammalian genomes

(2013) Adam D Ewing et al.   GENOME BIOLOGY

Newly evolved introns in human retrogenes provide novel insights into their evolutionary roles

(2012) Li-Fang Kang et al.   BMC EVOLUTIONARY BIOLOGY

Retrogenes Moved Out of the Z Chromosome in the Silkworm

(2012) Jun Wang et al.   JOURNAL OF MOLECULAR EVOLUTION

"Orphan" Retrogenes in the Human Genome

(2012) J. Ciomborowska et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mutations in the Mitochondrial Methionyl-tRNA Synthetase Cause a Neurodegenerative Phenotype in Flies and a Recessive Ataxia (ARSAL) in Humans

(2012) Vafa Bayat et al.   PLOS BIOLOGY

The GENCODE pseudogene resource

(2012) Baikang Pei et al.   GENOME BIOLOGY

A cautionary note for retrocopy identification: DNA-based duplication of intron-containing genes significantly contributes to the origination of single exon genes

(2011) Yong E. Zhang et al.   BIOINFORMATICS

Inferring the History of Interchromosomal Gene Transposition in Drosophila Using n -Dimensional Parsimony

(2011) Mira V. Han et al.   GENETICS

Role of Testis-Specific Gene Expression in Sex-Chromosome Evolution ofAnopheles gambiae

(2011) Dean A. Baker et al.   GENETICS

Retrogenes in Rice (Oryza sativa L. ssp. japonica) Exhibit Correlated Expression with Their Source Genes

(2011) Hiroaki Sakai et al.   Genome Biology and Evolution

No Excess Gene Movement Is Detected off the Avian or Lepidopteran Z Chromosome

(2011) Melissa A. Toups et al.   Genome Biology and Evolution

Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster

(2011) D. R. Schrider et al.   GENOME RESEARCH

Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease

(2011) C. Casola et al.   GENOME RESEARCH

Birth, Death, and Replacement of Karyopherins in Drosophila

(2011) N. Phadnis et al.   MOLECULAR BIOLOGY AND EVOLUTION

Dynamic interactions between transposable elements and their hosts

(2011) Henry L. Levin et al.   NATURE REVIEWS GENETICS

Evolutionary Patterns of RNA-Based Duplication in Non-Mammalian Chordates

(2011) Ming Chen et al.   PLoS One

Intralocus sexual conflict resolved through gene duplication

(2011) Miguel Gallach et al.   TRENDS IN ECOLOGY & EVOLUTION

A Detailed History of Intron-rich Eukaryotic Ancestors Inferred from a Global Survey of 100 Complete Genomes

(2011) Miklos Csuros et al.   PLoS Computational Biology

Genome-Wide Crossover Distribution in Arabidopsis thaliana Meiosis Reveals Sex-Specific Patterns along Chromosomes

(2011) Laurène Giraut et al.   PLoS Genetics

Frequent and recent retrotransposition of orthologous genes plays a role in the evolution of sperm glycolytic enzymes

(2010) Soumya A Vemuganti et al.   BMC GENOMICS

The rapid generation of chimerical genes expanding protein diversity in zebrafish

(2010) Beide Fu et al.   BMC GENOMICS

Drcd-1 related: a positively selected spermatogenesis retrogene in Drosophila

(2010) Jorge Ernesto Quezada-Díaz et al.   GENETICA

Convergently Recruited Nuclear Transport Retrogenes Are Male Biased in Expression and Evolving Under Positive Selection in Drosophila

(2010) C. Tracy et al.   GENETICS

Retrogenes Reveal the Direction of Sex-Chromosome Evolution in Mosquitoes

(2010) M. A. Toups et al.   GENETICS

Analyses of Nuclearly Encoded Mitochondrial Genes Suggest Gene Duplication as a Mechanism for Resolving Intralocus Sexually Antagonistic Conflict in Drosophila

(2010) Miguel Gallach et al.   Genome Biology and Evolution

Age-dependent chromosomal distribution of male-biased genes in Drosophila

(2010) Y. E. Zhang et al.   GENOME RESEARCH

Origins, evolution, and phenotypic impact of new genes

(2010) H. Kaessmann   GENOME RESEARCH

Primate and Rodent Specific Intron Gains and the Origin of Retrogenes with Splice Variants

(2010) Michał W Szcześniak et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inference for the Initial Stage of Domain Shuffling: Tracing the Evolutionary Fate of the PIPSL Retrogene in Hominoids

(2010) K. Ohshima et al.   MOLECULAR BIOLOGY AND EVOLUTION

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

The evolution of gene duplications: classifying and distinguishing between models

(2010) Hideki Innan et al.   NATURE REVIEWS GENETICS

Bs1, a New Chimeric Gene Formed by Retrotransposon-Mediated Exon Shuffling in Maize

(2010) N. Elrouby et al.   PLANT PHYSIOLOGY

Phosphoglycerate Kinase 2 (PGK2) Is Essential for Sperm Function and Male Fertility in Mice1

(2009) Polina V. Danshina et al.   BIOLOGY OF REPRODUCTION

A Complex Suite of Forces Drives Gene Traffic from Drosophila X Chromosomes

(2009) Richard P. Meisel et al.   Genome Biology and Evolution

General gene movement off the X chromosome in the Drosophila genus

(2009) M. D. Vibranovski et al.   GENOME RESEARCH

The Birth of New Genes by RNA- and DNA-Mediated Duplication during Mammalian Evolution

(2009) Jin Jun et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Distinguishing Among Evolutionary Models for the Maintenance of Gene Duplicates

(2009) M. W. Hahn   JOURNAL OF HEREDITY

Evolutionary Origin and Functions of Retrogene Introns

(2009) M. Fablet et al.   MOLECULAR BIOLOGY AND EVOLUTION

Discovery of short pseudogenes derived from messenger RNAs

(2009) Goro Terai et al.   NUCLEIC ACIDS RESEARCH

Extensive Structural Renovation of Retrogenes in the Evolution of the Populus Genome

(2009) Z. Zhu et al.   PLANT PHYSIOLOGY

Evolution of a Novel Phenolic Pathway for Pollen Development

(2009) M. Matsuno et al.   SCIENCE

Genetic conflict and sex chromosome evolution

(2009) Colin D. Meiklejohn et al.   TRENDS IN ECOLOGY & EVOLUTION

The emergence of new genes on the young therian X

(2009) Lukasz Potrzebowski et al.   TRENDS IN GENETICS

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

(2009) Xingyi Guo et al.   PLoS Computational Biology

Stage-Specific Expression Profiling of Drosophila Spermatogenesis Suggests that Meiotic Sex Chromosome Inactivation Drives Genomic Relocation of Testis-Expressed Genes

(2009) Maria D. Vibranovski et al.   PLoS Genetics

Evolutionary origin of regulatory regions of retrogenes in Drosophila

(2008) Yongsheng Bai et al.   BMC GENOMICS

Retrocopy contributions to the evolution of the human genome

(2008) Robert Baertsch et al.   BMC GENOMICS

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

Identification and analysis of ancestral hominoid transcriptome inferred from cross-species transcript and processed pseudogene comparisons

(2008) Y.-T. Huang et al.   GENOME RESEARCH

Genome analysis of the platypus reveals unique signatures of evolution

(2008) Wesley C. Warren et al.   NATURE

Endogenous siRNAs from naturally formed dsRNAs regulate transcripts in mouse oocytes

(2008) Toshiaki Watanabe et al.   NATURE

Pseudogene-derived small interfering RNAs regulate gene expression in mouse oocytes

(2008) Oliver H. Tam et al.   NATURE

Mouse segmental duplication and copy number variation

(2008) Xinwei She et al.   NATURE GENETICS

RNA-based gene duplication: mechanistic and evolutionary insights

(2008) Henrik Kaessmann et al.   NATURE REVIEWS GENETICS

The evolution of courtship behaviors through the origination of a new gene in Drosophila

(2008) H. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TRIMCyp expression in Old World primates Macaca nemestrina and Macaca fascicularis

(2008) G. Brennan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Independent genesis of chimeric TRIM5-cyclophilin proteins in two primate species

(2008) C. A. Virgen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary steps of sex chromosomes are reflected in retrogenes

(2008) Aoife McLysaght   TRENDS IN GENETICS

Where Do Introns Come From?

(2008) Francesco Catania et al.   PLOS BIOLOGY

Birth and Rapid Subcellular Adaptation of a Hominoid-Specific CDC14 Protein

(2008) Lia Rosso et al.   PLOS BIOLOGY

Chromosomal Gene Movements Reflect the Recent Origin and Biology of Therian Sex Chromosomes

(2008) Lukasz Potrzebowski et al.   PLOS BIOLOGY

Mitochondrial Targeting Adaptation of the Hominoid-Specific Glutamate Dehydrogenase Driven by Positive Darwinian Selection

(2008) Lia Rosso et al.   PLoS Genetics