Literature DB >> 24709753

Comparative primate genomics: emerging patterns of genome content and dynamics.

Jeffrey Rogers1, Richard A Gibbs1.   

Abstract

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

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Year:  2014        PMID： 24709753      PMCID： PMC4113315          DOI： 10.1038/nrg3707

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN： 1471-0056            Impact factor:   53.242


  106 in total

Review 1.  Hybridization and speciation.

Authors:  R Abbott; D Albach; S Ansell; J W Arntzen; S J E Baird; N Bierne; J Boughman; A Brelsford; C A Buerkle; R Buggs; R K Butlin; U Dieckmann; F Eroukhmanoff; A Grill; S H Cahan; J S Hermansen; G Hewitt; A G Hudson; C Jiggins; J Jones; B Keller; T Marczewski; J Mallet; P Martinez-Rodriguez; M Möst; S Mullen; R Nichols; A W Nolte; C Parisod; K Pfennig; A M Rice; M G Ritchie; B Seifert; C M Smadja; R Stelkens; J M Szymura; R Väinölä; J B W Wolf; D Zinner
Journal:  J Evol Biol       Date:  2013-02       Impact factor: 2.411

2.  CRHR1 genotypes, neural circuits and the diathesis for anxiety and depression.

Authors:  J Rogers; M Raveendran; G L Fawcett; A S Fox; S E Shelton; J A Oler; J Cheverud; D M Muzny; R A Gibbs; R J Davidson; N H Kalin
Journal:  Mol Psychiatry       Date:  2012-11-13       Impact factor: 15.992

3.  Genome-wide inference of natural selection on human transcription factor binding sites.

Authors:  Leonardo Arbiza; Ilan Gronau; Bulent A Aksoy; Melissa J Hubisz; Brad Gulko; Alon Keinan; Adam Siepel
Journal:  Nat Genet       Date:  2013-06-09       Impact factor: 38.330

4.  Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons.

Authors:  Genesio M Karere; Jeremy P Glenn; John L VandeBerg; Laura A Cox
Journal:  BMC Genomics       Date:  2012-07-18       Impact factor: 3.969

5.  An integrative variant analysis pipeline for accurate genotype/haplotype inference in population NGS data.

Authors:  Yi Wang; James Lu; Jin Yu; Richard A Gibbs; Fuli Yu
Journal:  Genome Res       Date:  2013-01-07       Impact factor: 9.043

6.  Great ape genetic diversity and population history.

Authors:  Javier Prado-Martinez; Peter H Sudmant; Jeffrey M Kidd; Heng Li; Joanna L Kelley; Belen Lorente-Galdos; Krishna R Veeramah; August E Woerner; Timothy D O'Connor; Gabriel Santpere; Alexander Cagan; Christoph Theunert; Ferran Casals; Hafid Laayouni; Kasper Munch; Asger Hobolth; Anders E Halager; Maika Malig; Jessica Hernandez-Rodriguez; Irene Hernando-Herraez; Kay Prüfer; Marc Pybus; Laurel Johnstone; Michael Lachmann; Can Alkan; Dorina Twigg; Natalia Petit; Carl Baker; Fereydoun Hormozdiari; Marcos Fernandez-Callejo; Marc Dabad; Michael L Wilson; Laurie Stevison; Cristina Camprubí; Tiago Carvalho; Aurora Ruiz-Herrera; Laura Vives; Marta Mele; Teresa Abello; Ivanela Kondova; Ronald E Bontrop; Anne Pusey; Felix Lankester; John A Kiyang; Richard A Bergl; Elizabeth Lonsdorf; Simon Myers; Mario Ventura; Pascal Gagneux; David Comas; Hans Siegismund; Julie Blanc; Lidia Agueda-Calpena; Marta Gut; Lucinda Fulton; Sarah A Tishkoff; James C Mullikin; Richard K Wilson; Ivo G Gut; Mary Katherine Gonder; Oliver A Ryder; Beatrice H Hahn; Arcadi Navarro; Joshua M Akey; Jaume Bertranpetit; David Reich; Thomas Mailund; Mikkel H Schierup; Christina Hvilsom; Aida M Andrés; Jeffrey D Wall; Carlos D Bustamante; Michael F Hammer; Evan E Eichler; Tomas Marques-Bonet
Journal:  Nature       Date:  2013-07-03       Impact factor: 49.962

7.  A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species.

Authors:  Thomas Mailund; Anders E Halager; Michael Westergaard; Julien Y Dutheil; Kasper Munch; Lars N Andersen; Gerton Lunter; Kay Prüfer; Aylwyn Scally; Asger Hobolth; Mikkel H Schierup
Journal:  PLoS Genet       Date:  2012-12-20       Impact factor: 5.917

8.  Incomplete lineage sorting is common in extant gibbon genera.

Authors:  Jeffrey D Wall; Sung K Kim; Francesca Luca; Lucia Carbone; Alan R Mootnick; Pieter J de Jong; Anna Di Rienzo
Journal:  PLoS One       Date:  2013-01-14       Impact factor: 3.240

9.  The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics.

Authors:  Lenore Pipes; Sheng Li; Marjan Bozinoski; Robert Palermo; Xinxia Peng; Phillip Blood; Sara Kelly; Jeffrey M Weiss; Jean Thierry-Mieg; Danielle Thierry-Mieg; Paul Zumbo; Ronghua Chen; Gary P Schroth; Christopher E Mason; Michael G Katze
Journal:  Nucleic Acids Res       Date:  2012-11-29       Impact factor: 16.971

10.  Baboon phylogeny as inferred from complete mitochondrial genomes.

Authors:  Dietmar Zinner; Jenny Wertheimer; Rasmus Liedigk; Linn F Groeneveld; Christian Roos
Journal:  Am J Phys Anthropol       Date:  2012-11-26       Impact factor: 2.868
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  93 in total

1.  Evolutionary insights from wild vervet genomes.

Authors:  Ellen M Leffler
Journal:  Nat Genet       Date:  2017-11-29       Impact factor: 38.330

2.  Novel MHC class I full-length allele and haplotype characterization in sooty mangabeys.

Authors:  Katelyn E Heimbruch; Julie A Karl; Roger W Wiseman; Dawn M Dudley; Zach Johnson; Amitinder Kaur; David H O'Connor
Journal:  Immunogenetics       Date:  2015-05-26       Impact factor: 2.846

Review 3.  The Genome 10K Project: a way forward.

Authors:  Klaus-Peter Koepfli; Benedict Paten; Stephen J O'Brien
Journal:  Annu Rev Anim Biosci       Date:  2015       Impact factor: 8.923

4.  Tau isoform expression and phosphorylation in marmoset brains.

Authors:  Govinda Sharma; Anni Huo; Taeko Kimura; Seiji Shiozawa; Reona Kobayashi; Naruhiko Sahara; Minaka Ishibashi; Shinsuke Ishigaki; Taro Saito; Kanae Ando; Shigeo Murayama; Masato Hasegawa; Gen Sobue; Hideyuki Okano; Shin-Ichi Hisanaga
Journal:  J Biol Chem       Date:  2019-06-05       Impact factor: 5.157

5.  Macrophages Are Phenotypically and Functionally Diverse across Tissues in Simian Immunodeficiency Virus-Infected and Uninfected Asian Macaques.

Authors:  Alexandra M Ortiz; Sarah R DiNapoli; Jason M Brenchley
Journal:  J Virol       Date:  2015-03-18       Impact factor: 5.103

6.  Population genetics of wild Macaca fascicularis with low-coverage shotgun sequencing of museum specimens.

Authors:  Lu Yao; Kelsey Witt; Hongjie Li; Jonathan Rice; Nelson R Salinas; Robert D Martin; Emilia Huerta-Sánchez; Ripan S Malhi
Journal:  Am J Phys Anthropol       Date:  2020-07-08       Impact factor: 2.868

Review 7.  Microbial control of host gene regulation and the evolution of host-microbiome interactions in primates.

Authors:  Laura Grieneisen; Amanda L Muehlbauer; Ran Blekhman
Journal:  Philos Trans R Soc Lond B Biol Sci       Date:  2020-08-10       Impact factor: 6.237

Review 8.  Use and Importance of Nonhuman Primates in Metabolic Disease Research: Current State of the Field.

Authors:  Peter J Havel; Paul Kievit; Anthony G Comuzzie; Andrew A Bremer
Journal:  ILAR J       Date:  2017-12-01

Review 9.  Enhancing our brains: Genomic mechanisms underlying cortical evolution.

Authors:  Caitlyn Mitchell; Debra L Silver
Journal:  Semin Cell Dev Biol       Date:  2017-08-31       Impact factor: 7.727

10.  The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming.

Authors:  Jens Durruthy-Durruthy; Vittorio Sebastiano; Mark Wossidlo; Diana Cepeda; Jun Cui; Edward J Grow; Jonathan Davila; Moritz Mall; Wing H Wong; Joanna Wysocka; Kin Fai Au; Renee A Reijo Pera
Journal:  Nat Genet       Date:  2015-11-23       Impact factor: 38.330
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