Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats
Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition.
Vyšlo v časopise:
Transposed Genes in Arabidopsis Are Often Associated with Flanking Repeats. PLoS Genet 6(5): e32767. doi:10.1371/journal.pgen.1000949
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1000949
Souhrn
Much of the eukaryotic genome is known to be mobile, largely due to the movement of transposons and other parasitic elements. Recent work in plants and Drosophila suggests that mobility is also a feature of many nontransposon genes and gene families. Indeed, analysis of the Arabidopsis genome suggested that as many as half of all genes had moved to unlinked positions since Arabidopsis diverged from papaya roughly 72 million years ago, and that these mobile genes tend to fall into distinct gene families. However, the mechanism by which single gene transposition occurred was not deduced. By comparing two closely related species, Arabidopsis thaliana and Arabidopsis lyrata, we sought to determine the nature of gene transposition in Arabidopsis. We found that certain categories of genes are much more likely to have transposed than others, and that many of these transposed genes are flanked by direct repeat sequence that was homologous to sequence within the orthologous target site in A. lyrata and which was predominantly genic in identity. We suggest that intrachromosomal recombination between tandemly duplicated sequences, and subsequent insertion of the circular product, is the predominant mechanism of gene transposition.
Zdroje
1. MeyersBC
2003 Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. The Plant cell 15 809 834
2. FreelingM
LyonsE
PedersenB
AlamM
MingR
2008 Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Res 18 1924 1937
3. YangSA
ArguelloJR
LiX
DingY
ZhouQ
2008 Repetitive element-mediated recombination as a mechanism for new gene origination in Drosophila. Plos Genet 4 e3 doi:10.1371/journal.pgen.0040003
4. MingR
HouS
FengY
YuQ
Dionne-LaporteA
2008 The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452 991 996
5. JiangN
BaoZ
ZhangX
EddySR
WesslerSR
2004 Pack-MULE transposable elements mediate gene evolution in plants. Nature 431 569 573
6. MontgomeryEA
HuangSM
LangleyCH
JuddBH
1991 Chromosome Rearrangement by Ectopic Recombination in Drosophila-Melanogaster - Genome Structure and Evolution. Genetics 129 1085 1098
7. MooreJK
HaberJE
1996 Cell cycle and genetic requirements of two pathyways of nonhomologous end-joining repair of double-strand breaks in Saccharomyces cerevisiae. Mo Cell Biol 16 2164 2173
8. KotchM
HauboldB
Mitchell-OldsT
2000 Comparative evolutionary analysis of chalcone synthase and alcohol dehydrogenase loci in Arabidopsis, Arabis and related genera. Mol Biol Evol 17 1483 1498
9. ZiolkowskiPA
KoczykG
GalganskiL
SadowskiJ
2009 Genome sequence comparison of Col and Ler lines reveals the dynamic nature of Arabidopsis chromosomes. Nucleic Acids Research 37 3189 3201
10. DevosKM
BrownJK
BennetzenJL
2002 Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12 1075 1079
11. LeisterD
2004 Tandem and segmental gene duplication and recombination in the evolution of plant disease resistance gene. Trends Genet 20 116 122
12. NobusatoA
UchiyamaI
OhashiS
KobayashiI
2000 Insertion with long target duplication: a mechanism for gene mobility suggested from comparison of two related bacterial genomes. Gene 259 99 108
13. MamedovIZ
LebedevYB
SverdlovED
2004 Unusually long target site duplications flanking some of the long terminal repeats of human endogenous retrovirus K in the human genome. Journal of General Virology 85 1485 1488
14. RizzonC
PongerL
GautBS
2006 Striking Similarities in the Genomic Distribution of Tandemly Arrayed Genes in Arabidopsis and Rice. PLoS Comput Biol 2 e115 doi:10.1371/journal.pcbi.0020115
15. ZhouQ
ZhangGJ
ZhangY
XuSY
ZhaoRP
2008 On the origin of new genes in Drosophila. Genome Research 18 1446 1455
16. RogersRL
BedfordT
HartlDL
2009 Formation and Longevity of Chimeric and Duplicate Genes in Drosophila melanogaster. Genetics 181 313 322
17. CohenS
HoubenA
SegalD
2008 Extrachromosomal circular DNA derived from tandemly repeated genomic sequences in plants. Plant Journal 53 1027 1034
18. CohenS
YacobiK
SegalD
2003 Extrachromosomal circular DNA of tandemly repeated genomic sequences in Drosophila. Genome Research 13 1133 1145
19. ParniskeM
JonesJD
1999 Recombination between diverged clusters of the tomato Cf-9 plant disease resistance gene family. Proc Natl Acad Sci 96 5850 5855
20. PetrovDA
ChaoYC
StephensonEC
HartlDL
1998 Pseudogene evolution in Drosophila suggests a high rate of DNA loss. Molecular Biology and Evolution 15 1562 1567
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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