Literature DB >> 18258610

The dynamic nature of eukaryotic genomes.

Laura Wegener Parfrey1, Daniel J G Lahr, Laura A Katz.   

Abstract

Analyses of diverse eukaryotes reveal that genomes are dynamic, sometimes dramatically so. In numerous lineages across the eukaryotic tree of life, DNA content varies within individuals throughout life cycles and among individuals within species. Discovery of examples of genome dynamism is accelerating as genome sequences are completed from diverse eukaryotes. Though much is known about genomes in animals, fungi, and plants, these lineages represent only 3 of the 60-200 lineages of eukaryotes. Here, we discuss diverse genomic strategies in exemplar eukaryotic lineages, including numerous microbial eukaryotes, to reveal dramatic variation that challenges established views of genome evolution. For example, in the life cycle of some members of the "radiolaria," ploidy increases from haploid (N) to approximately 1,000N, whereas intrapopulation variability of the enteric parasite Entamoeba ranges from 4N to 40N. Variation has also been found within our own species, with substantial differences in both gene content and chromosome lengths between individuals. Data on the dynamic nature of genomes shift the perception of the genome from being fixed and characteristic of a species (typological) to plastic due to variation within and between species.

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Year:  2008        PMID: 18258610      PMCID: PMC2933061          DOI: 10.1093/molbev/msn032

Source DB:  PubMed          Journal:  Mol Biol Evol        ISSN: 0737-4038            Impact factor:   16.240


  66 in total

1.  A kingdom-level phylogeny of eukaryotes based on combined protein data.

Authors:  S L Baldauf; A J Roger; I Wenk-Siefert; W F Doolittle
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Review 2.  Genetic processes in arbuscular mycorrhizal fungi.

Authors:  Teresa E Pawlowska
Journal:  FEMS Microbiol Lett       Date:  2005-10-15       Impact factor: 2.742

3.  Peculiar behavior of distinct chromosomal DNA elements during and after development in the dicyemid mesozoan Dicyema japonicum.

Authors:  Hiroko Awata; Tomoko Noto; Hiroshi Endoh
Journal:  Chromosome Res       Date:  2007-01-19       Impact factor: 5.239

4.  Genome diversity in microbial eukaryotes.

Authors:  Casey L McGrath; Laura A Katz
Journal:  Trends Ecol Evol       Date:  2004-01       Impact factor: 17.712

Review 5.  Epigenetics: a landscape takes shape.

Authors:  Aaron D Goldberg; C David Allis; Emily Bernstein
Journal:  Cell       Date:  2007-02-23       Impact factor: 41.582

6.  Chromatin diminution in the copepod Mesocyclops edax: diminution of tandemly repeated DNA families from somatic cells.

Authors:  Guy Drouin
Journal:  Genome       Date:  2006-06       Impact factor: 2.166

7.  Genome ploidy in different stages of the Giardia lamblia life cycle.

Authors:  R Bernander; J E Palm; S G Svärd
Journal:  Cell Microbiol       Date:  2001-01       Impact factor: 3.715

8.  The biochemical composition of the free-living amoebae Chaos chaos, Amoeba dubia and Amoeba proteus.

Authors:  C T Friz
Journal:  Comp Biochem Physiol       Date:  1968-07

9.  The synthesis of DNA through the cell cycle of Amoeba proteus.

Authors:  M J Ord
Journal:  J Cell Sci       Date:  1968-12       Impact factor: 5.285

10.  Macronuclear genome sequence of the ciliate Tetrahymena thermophila, a model eukaryote.

Authors:  Jonathan A Eisen; Robert S Coyne; Martin Wu; Dongying Wu; Mathangi Thiagarajan; Jennifer R Wortman; Jonathan H Badger; Qinghu Ren; Paolo Amedeo; Kristie M Jones; Luke J Tallon; Arthur L Delcher; Steven L Salzberg; Joana C Silva; Brian J Haas; William H Majoros; Maryam Farzad; Jane M Carlton; Roger K Smith; Jyoti Garg; Ronald E Pearlman; Kathleen M Karrer; Lei Sun; Gerard Manning; Nels C Elde; Aaron P Turkewitz; David J Asai; David E Wilkes; Yufeng Wang; Hong Cai; Kathleen Collins; B Andrew Stewart; Suzanne R Lee; Katarzyna Wilamowska; Zasha Weinberg; Walter L Ruzzo; Dorota Wloga; Jacek Gaertig; Joseph Frankel; Che-Chia Tsao; Martin A Gorovsky; Patrick J Keeling; Ross F Waller; Nicola J Patron; J Michael Cherry; Nicholas A Stover; Cynthia J Krieger; Christina del Toro; Hilary F Ryder; Sondra C Williamson; Rebecca A Barbeau; Eileen P Hamilton; Eduardo Orias
Journal:  PLoS Biol       Date:  2006-09       Impact factor: 8.029

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  52 in total

1.  Evolution of germline-limited sequences in two populations of the ciliate Chilodonella uncinata.

Authors:  Rebecca A Zufall; Mariel Sturm; Brian C Mahon
Journal:  J Mol Evol       Date:  2012-03-13       Impact factor: 2.395

2.  The energetics of genome complexity.

Authors:  Nick Lane; William Martin
Journal:  Nature       Date:  2010-10-21       Impact factor: 49.962

Review 3.  The chastity of amoebae: re-evaluating evidence for sex in amoeboid organisms.

Authors:  Daniel J G Lahr; Laura Wegener Parfrey; Edward A D Mitchell; Laura A Katz; Enrique Lara
Journal:  Proc Biol Sci       Date:  2011-03-23       Impact factor: 5.349

4.  Disentangling sources of variation in SSU rDNA sequences from single cell analyses of ciliates: impact of copy number variation and experimental error.

Authors:  Chundi Wang; Tengteng Zhang; Yurui Wang; Laura A Katz; Feng Gao; Weibo Song
Journal:  Proc Biol Sci       Date:  2017-07-26       Impact factor: 5.349

5.  Evolution of the actin gene family in testate lobose amoebae (Arcellinida) is characterized by two distinct clades of paralogs and recent independent expansions.

Authors:  Daniel J G Lahr; Truc B Nguyen; Erika Barbero; Laura A Katz
Journal:  Mol Biol Evol       Date:  2010-08-02       Impact factor: 16.240

Review 6.  Blank spots on the map: some current questions on nuclear organization and genome architecture.

Authors:  Carmen Adriaens; Leonid A Serebryannyy; Marina Feric; Andria Schibler; Karen J Meaburn; Nard Kubben; Pawel Trzaskoma; Sigal Shachar; Sandra Vidak; Elizabeth H Finn; Varun Sood; Gianluca Pegoraro; Tom Misteli
Journal:  Histochem Cell Biol       Date:  2018-09-20       Impact factor: 4.304

Review 7.  How discordant morphological and molecular evolution among microorganisms can revise our notions of biodiversity on Earth.

Authors:  Daniel J G Lahr; Haywood Dail Laughinghouse; Angela M Oliverio; Feng Gao; Laura A Katz
Journal:  Bioessays       Date:  2014-08-25       Impact factor: 4.345

8.  Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data.

Authors:  Chuming Chen; Peter B McGarvey; Hongzhan Huang; Cathy H Wu
Journal:  Adv Bioinformatics       Date:  2010-03-29

9.  Genome dynamics are influenced by food source in Allogromia laticollaris strain CSH (Foraminifera).

Authors:  Laura Wegener Parfrey; Laura A Katz
Journal:  Genome Biol Evol       Date:  2010-08-13       Impact factor: 3.416

10.  Inter-cellular variation in DNA content of Entamoeba histolytica originates from temporal and spatial uncoupling of cytokinesis from the nuclear cycle.

Authors:  Chandrama Mukherjee; Shubhra Majumder; Anuradha Lohia
Journal:  PLoS Negl Trop Dis       Date:  2009-04-07
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