Widespread duplications in the genomes of laboratory stocks of Dictyostelium discoideum.

Genome Biology
Gareth BloomfieldRobert R Kay

Abstract

Duplications of stretches of the genome are an important source of individual genetic variation, but their unrecognized presence in laboratory organisms would be a confounding variable for genetic analysis. We report here that duplications of 15 kb or more are common in the genome of the social amoeba Dictyostelium discoideum. Most stocks of the axenic 'workhorse' strains Ax2 and Ax3/4 obtained from different laboratories can be expected to carry different duplications. The auxotrophic strains DH1 and JH10 also bear previously unreported duplications. Strain Ax3/4 is known to carry a large duplication on chromosome 2 and this structure shows evidence of continuing instability; we find a further variable duplication on chromosome 5. These duplications are lacking in Ax2, which has instead a small duplication on chromosome 1. Stocks of the type isolate NC4 are similarly variable, though we have identified some approximating the assumed ancestral genotype. More recent wild-type isolates are almost without large duplications, but we can identify small deletions or regions of high divergence, possibly reflecting responses to local selective pressures. Duplications are scattered through most of the genome, and can be stable enough to...Continue Reading

References

Aug 1, 1979·Journal of General Microbiology·M A Wallace, K B Raper
Jan 1, 1978·Annual Review of Genetics·P C Newell
Sep 15, 1992·Proceedings of the National Academy of Sciences of the United States of America·A Kuspa, W F Loomis
Apr 1, 1991·Genes & Development·T J Sun, P N Devreotes
Oct 5, 1990·Journal of Molecular Biology·S F AltschulD J Lipman
Nov 1, 1990·Proceedings of the National Academy of Sciences of the United States of America·E C CoxE S Bain
Sep 1, 1970·The Biochemical Journal·D J Watts, J M Ashworth
Feb 1, 1971·Experimental Cell Research·W F Loomis
Jul 11, 2000·Nature Genetics·T R HughesM J Marton
Apr 3, 2001·Genome Research·G GlöcknerA Rosenthal
Mar 26, 2002·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Charles KooperbergToshio Tsukiyama
Jul 5, 2002·Nature·Gernot GlöcknerUNKNOWN Dictyostelium Genome Sequencing Consortium
Sep 26, 2002·Proceedings of the National Academy of Sciences of the United States of America·Jonathan R PollackPatrick O Brown
Nov 26, 2002·Proceedings of the National Academy of Sciences of the United States of America·Maitreya J DunhamDavid Botstein
Nov 1, 2003·Science·A B SingletonK Gwinn-Hardy
Jul 27, 2004·Science·Jonathan SebatMichael Wigler
Aug 3, 2004·Nature Genetics·A John IafrateCharles Lee
Aug 24, 2004·Nature Genetics·Jiangzhen LiWei-Wen Cai
Sep 3, 2004·Development·Christina SchildeJeffrey G Williams
Feb 25, 2005·Molecular Biology of the Cell·Scott A MyersChang Y Chung
May 6, 2005·Nature·L EichingerA Kuspa
Feb 21, 2006·Cancer Research·Dafna TsafrirDaniel A Notterman
Aug 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·M L GoldbergM M Green
May 2, 2006·Statistical Applications in Genetics and Molecular Biology·Gordon K Smyth
Jul 11, 2006·European Journal of Cell Biology·Alice Y PollittRobert H Insall
Jul 22, 2006·Science·Anna SelmeckiJudith Berman
Aug 10, 2006·Eukaryotic Cell·Yi Liu, Deborah Bell-Pedersen
Oct 31, 2006·Nature Genetics·Cédric Le MaréchalClaude Férec
Nov 24, 2006·Nature·Richard RedonMatthew E Hurles
Jan 20, 2007·Bioinformatics·E S Venkatraman, Adam B Olshen
Feb 10, 2007·Science·Barbara E StrangerEmmanouil T Dermitzakis

❮ Previous
Next ❯

Citations

May 12, 2010·The Journal of Biological Chemistry·Christopher SugdenJeffrey G Williams
Jun 28, 2012·The Journal of Biological Chemistry·Venketesh Sivaramakrishnan, Samuel J Fountain
Jun 11, 2010·Molecular Biology of the Cell·Regina TeoAdrian J Harwood
Jan 31, 2009·Nucleic Acids Research·Gernot Glöckner, Andrew J Heidel
Dec 15, 2010·Science·Gareth BloomfieldRobert R Kay
Feb 21, 2009·BMC Cell Biology·Alice Y Pollitt, Robert H Insall
Jan 25, 2011·BMC Developmental Biology·David M GreeneCatherine J Pears
May 16, 2009·BMC Evolutionary Biology·Paweł Mackiewicz, Elzbieta Wyroba
Sep 3, 2010·Journal of Cell Science·Roberto ZanchiRobert R Kay
Feb 27, 2010·PloS One·Maria Christina ShinaWaldemar Kolanus
Mar 13, 2014·The Journal of Cell Biology·Evgeny ZatulovskiyRobert R Kay
Jan 23, 2016·Development Genes and Evolution·Johanna Márquez LópezSascha Thewes
Mar 2, 2016·Nature Communications·Xuezhi ZhangThierry Soldati
Mar 17, 2015·Journal of Evolutionary Biology·S R LevinJ E Strassmann
Jan 19, 2010·Developmental Biology·Yoko YamadaJeffrey G Williams
Sep 15, 2009·Cell Host & Microbe·Zhiru LiRalph R Isberg
Mar 31, 2015·ELife·Gareth BloomfieldRobert R Kay
Mar 15, 2011·Developmental Biology·Christopher SugdenJeffrey G Williams
Dec 14, 2016·ELife·Douwe M VeltmanRobert R Kay
Sep 11, 2019·Genome Biology and Evolution·Joshua J Faber-HammondSuzy C P Renn
Jul 28, 2020·Frontiers in Cell and Developmental Biology·Megan M AokiRobert J Huber
Apr 11, 2019·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Thomas D WilliamsRobert R Kay
Mar 13, 2020·Proceedings of the National Academy of Sciences of the United States of America·Sven FlemmingCarsten Beta
Jan 1, 2008·CSH Protocols·Pascale GaudetRex Chisholm

❮ Previous
Next ❯

Datasets Mentioned

BETA
E-TABM-394

Methods Mentioned

BETA
electrophoresis
PCR

Software Mentioned

Limma
BLAST
Genepix

Related Concepts

Related Feeds

Candidiasis

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Candidiasis (ASM)

Candidiasis is a common fungal infection caused by Candida and it can affect many parts for the body including mucosal membranes as well as the gastrointestinal, urinary, and respiratory tracts. Here is the latest research.

Candida albicans

Candida albicans is an opportunistic, fungal pathogen of humans that frequently causes superficial infections of oral and vaginal mucosal surfaces of debilitated and susceptible individuals. Discover the latest research on Candida albicans here.