Table III.2. Natural Genetic Engineering Documented in the Evolution of Sequenced Genomes.

Rearrangement feature(s) noted

Reference

Pack-MULE transposons mediating coding sequence duplications and exon shuffling in rice

(Jiang, Bao et al. 2004; Hanada, Vallejo et al. 2009)

Exon shuffling by a CACTA transposon in beans (glycine max)

(Zabala and Vodkin 2007)

Exon shuffling and amplification by helitrons in maize

(Gupta, Gallavotti et al. 2005; Lai, Li et al. 2005; Morgante, Brunner et al. 2005; Xu and Messing 2006; Jameson, Georgelis et al. 2008)

Exon origination in coffee and Arabidopsis from transposable elements

(Lopes, Carazzolle et al. 2008)

The Hobo transposon involved in endemic inversions in natural Drosophila populations

(Lyttle and Haymer 1992)

Gross chromosome rearrangements mediated by transposable elements in Drosophila melanogaster; the data include natural populations

(Lim and Simmons 1994)

Generation of a widespread Drosophila buzzatii inversion by a transposable element; two natural hotspots and multiple other rearrangements in the Drosophila buzzatii genome induced by the Gallileo transposon

(Caceres, Ranz et al. 1999; Caceres, Puig et al. 2001; Delprat, Negre et al. 2009)

Penelope and Ulysses retroelements involved in Drosophila virilis chromosome rearrangements at natural breakpoints

(Evgen'ev, Zelentsova et al. 2000; Evgen'ev, Zelentsova et al. 2000)

Chromosome rearrangements involving two transposons

(Gray 2000)

Reviews role of hotspots in transposon-generated chromosome rearrangements

(Lonnig and Saedler 2002)

Abundance and recent occurrence of segmental duplications in the human genome

(Samonte and Eichler 2002)

Segmental duplications found at syntenic region breakpoints in human and mouse genomes

(Bailey, Baertsch et al. 2004)

Review role of transposable elements as chromosome rearrangement catalysts

(Bourque 2009; Zhao and Bourque 2009)

Richness of transposable elements in Drosophila pericentric heterochromatin

(Bergman, Quesneville et al. 2006)

Novel transposable element insertions found near loci encoding insecticide-metabolizing enzymes in Drosophila

(Chen and Li 2007)

Segmental duplication associated with a chromosome inversion in malaria mosquito vector

(Coulibaly, Lobo et al. 2007)

Dispersed LINE and SINE repeats in the human genome as substrates for ectopic homologous recombination

(Gu, Zhang et al. 2008)

Coincidence of primate syntenic breakpoints with presence of transposable elements

(Kehrer-Sawatzki and Cooper 2008)

LINE-1 elements associated with deletions in human genome variation

(Han, Lee et al. 2008)

DS breaks associated with repetitive DNA in yeast

  (Argueso, Westmoreland et al. 2008)

Many inversions associated with L1 repeats

 (Zhao and Bourque 2009)

Syntenic breakpoints between human and gibbon genomes showed new insertions of gibbon-specific repeats and mosaic structures involving segmental duplications, LINE, SINE, and LTR elements

 (Girirajan, Chen et al. 2009)

Chromosome rearrangements by Ty element recombinations in a wild strain of yeast used for wine fermentation

(Rachidi, Barre et al. 1999)

Evolutionary breakpoints in Wallaby genome associated with SINEs, LINEs and endogenous retroviruses

(Longo, Carone et al. 2009)

P element insertions next to heat shock promoters in wild Drosophila

(Shilova, Garbuz et al. 2006; Haney and Feder 2009)