Literature DB >> 15599514

Shedding genomic ballast: extensive parallel loss of ancestral gene families in animals.

Austin L Hughes1, Robert Friedman.   

Abstract

Loss of ancestral gene families has played an important role in genomic specialization in animals. An examination of the pattern of gene family loss in completely sequenced animal genomes revealed that the same gene families have been lost independently in different lineages to a far greater extent than expected if gene loss occurred at random. This result implies that certain ancestral gene families-and thus the biological functions they encode-have been more expendable than others over the radiation of the animal phyla.

Mesh:

Year:  2004        PMID: 15599514     DOI: 10.1007/s00239-004-0115-7

Source DB:  PubMed          Journal:  J Mol Evol        ISSN: 0022-2844            Impact factor:   2.395


  31 in total

1.  Genes lost during evolution.

Authors:  J Roelofs; P J Van Haastert
Journal:  Nature       Date:  2001-06-28       Impact factor: 49.962

2.  Microbial genes in the human genome: lateral transfer or gene loss?

Authors:  S L Salzberg; O White; J Peterson; J A Eisen
Journal:  Science       Date:  2001-05-17       Impact factor: 47.728

3.  Recent segmental duplications in the human genome.

Authors:  Jeffrey A Bailey; Zhiping Gu; Royden A Clark; Knut Reinert; Rhea V Samonte; Stuart Schwartz; Mark D Adams; Eugene W Myers; Peter W Li; Evan E Eichler
Journal:  Science       Date:  2002-08-09       Impact factor: 47.728

4.  Parallel evolution by gene duplication in the genomes of two unicellular fungi.

Authors:  Austin L Hughes; Robert Friedman
Journal:  Genome Res       Date:  2003-05       Impact factor: 9.043

5.  Gene prediction by pattern recognition and homology search.

Authors:  Y Xu; E C Uberbacher
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  1996

6.  Complete sequence analysis of the genome of the bacterium Mycoplasma pneumoniae.

Authors:  R Himmelreich; H Hilbert; H Plagens; E Pirkl; B C Li; R Herrmann
Journal:  Nucleic Acids Res       Date:  1996-11-15       Impact factor: 16.971

7.  A new method of inference of ancestral nucleotide and amino acid sequences.

Authors:  Z Yang; S Kumar; M Nei
Journal:  Genetics       Date:  1995-12       Impact factor: 4.562

8.  Early evolution of the bilateria.

Authors:  B Hausdorf
Journal:  Syst Biol       Date:  2000-03       Impact factor: 15.683

9.  A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

Authors:  Eugene V Koonin; Natalie D Fedorova; John D Jackson; Aviva R Jacobs; Dmitri M Krylov; Kira S Makarova; Raja Mazumder; Sergei L Mekhedov; Anastasia N Nikolskaya; B Sridhar Rao; Igor B Rogozin; Sergei Smirnov; Alexander V Sorokin; Alexander V Sverdlov; Sona Vasudevan; Yuri I Wolf; Jodie J Yin; Darren A Natale
Journal:  Genome Biol       Date:  2004-01-15       Impact factor: 13.583

10.  A molecular timescale of eukaryote evolution and the rise of complex multicellular life.

Authors:  S Blair Hedges; Jaime E Blair; Maria L Venturi; Jason L Shoe
Journal:  BMC Evol Biol       Date:  2004-01-28       Impact factor: 3.260

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  15 in total

1.  Selectionism and neutralism in molecular evolution.

Authors:  Masatoshi Nei
Journal:  Mol Biol Evol       Date:  2005-08-24       Impact factor: 16.240

2.  Evolutionary change of the numbers of homeobox genes in bilateral animals.

Authors:  Jongmin Nam; Masatoshi Nei
Journal:  Mol Biol Evol       Date:  2005-08-03       Impact factor: 16.240

Review 3.  Convergent evolution of defensin sequence, structure and function.

Authors:  Thomas M A Shafee; Fung T Lay; Thanh Kha Phan; Marilyn A Anderson; Mark D Hulett
Journal:  Cell Mol Life Sci       Date:  2016-08-24       Impact factor: 9.261

4.  Genome size reduction in the chicken has involved massive loss of ancestral protein-coding genes.

Authors:  Austin L Hughes; Robert Friedman
Journal:  Mol Biol Evol       Date:  2008-09-26       Impact factor: 16.240

5.  Genetic resources for maize cell wall biology.

Authors:  Bryan W Penning; Charles T Hunter; Reuben Tayengwa; Andrea L Eveland; Christopher K Dugard; Anna T Olek; Wilfred Vermerris; Karen E Koch; Donald R McCarty; Mark F Davis; Steven R Thomas; Maureen C McCann; Nicholas C Carpita
Journal:  Plant Physiol       Date:  2009-11-19       Impact factor: 8.340

6.  Strong functional patterns in the evolution of eukaryotic genomes revealed by the reconstruction of ancestral protein domain repertoires.

Authors:  Christian M Zmasek; Adam Godzik
Journal:  Genome Biol       Date:  2011-01-17       Impact factor: 13.583

7.  GLADX: an automated approach to analyze the lineage-specific loss and pseudogenization of genes.

Authors:  Jacques Dainat; Julien Paganini; Pierre Pontarotti; Philippe Gouret
Journal:  PLoS One       Date:  2012-06-18       Impact factor: 3.240

8.  Conservation and co-option in developmental programmes: the importance of homology relationships.

Authors:  Matthias Sanetra; Gerrit Begemann; May-Britt Becker; Axel Meyer
Journal:  Front Zool       Date:  2005-10-10       Impact factor: 3.172

9.  Invertebrate 7SK snRNAs.

Authors:  Andreas R Gruber; Dorota Koper-Emde; Manja Marz; Hakim Tafer; Stephan Bernhart; Gregor Obernosterer; Axel Mosig; Ivo L Hofacker; Peter F Stadler; Bernd-Joachim Benecke
Journal:  J Mol Evol       Date:  2008-01-12       Impact factor: 2.395

10.  Duplication and population dynamics shape historic patterns of selection and genetic variation at the major histocompatibility complex in rodents.

Authors:  Jamie C Winternitz; John P Wares
Journal:  Ecol Evol       Date:  2013-04-22       Impact factor: 2.912

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