A Microarray Based Genomic Hybridization Method for Identification of New Genes in Plants: Case Analyses of Arabidopsis and Oryza

To systematically estimate the gene duplication events in closely related species, we have to use comparative genomic approaches, either through genomic sequence comparison or comparative genomic hybridization (CGH). Given the scarcity of complete genomic sequences of plant species, in the present study we adopted an array based CGH to investigate gene duplications in the genus Arabidopsis. Fragment genomic DNA from four species, namely Arabidopsis thaliana, A. lyrata subsp. lyrata, A. lyrata subsp. petraea, and A. halleri, was hybridized to Affymetrix (Santa Clara, CA, USA) tiling arrays that are designed from the genomic sequences of A. thaliana. Pairwise comparisons of signal intensity were made to infer the potential duplicated candidates along each phylogenetic branch. Ninety-four potential candidates of gene duplication along the genus were identified. Among them, the majority (69 of 94) were A. thaliana lineage specific. This result indicates that the array based CGH approach may be used to identify candidates of duplication in other plant genera containing closely related species, such as Oryza, particularly for the AA genome species. We compared the degree of gene duplication through retrotransposon between O. sativa and A. thaliana and found a strikingly higher number of chimera retroposed genes in rice. The higher rate of gene duplication through retroposition and other mechanisms may indicate that the grass species is able to adapt to more diverse environments.

[1]  Dr. Susumu Ohno.  Evolution by Gene Duplication , 1970, Springer Berlin Heidelberg.

[2]  W. Gilbert.  Why genes in pieces? , 1978, Nature.

[3]  M. Kimura.  The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[4]  J. Brosius,et al.  Retroposons--seeds of evolution. , 1991, Science.

[5]  D. Labuda,et al.  Alu sequences in the coding regions of mRNA: a source of protein variability. , 1994, Trends in genetics : TIG.

[6]  A. Hughes.  The evolution of functionally novel proteins after gene duplication , 1994, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[7]  W. Gilbert,et al.  Exon shuffling and the origin of the mitochondrial targeting function in plant cytochrome c1 precursor. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[8]  The Arabidopsis Genome Initiative.  Analysis of the genome sequence of the flowering plant Arabidopsis thaliana , 2000, Nature.

[9]  H. Ochman,et al.  Lateral and oblique gene transfer. , 2001, Current opinion in genetics & development.

[10]  Kevin R. Thornton,et al.  The origin of new genes: glimpses from the young and old , 2003, Nature Reviews Genetics.

[11]  Detlef Weigel,et al.  Large-scale identification of single-feature polymorphisms in complex genomes. , 2003, Genome research.

[12]  John D. Storey,et al.  Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[13]  W. Martin,et al.  Endosymbiotic gene transfer: organelle genomes forge eukaryotic chromosomes , 2004, Nature Reviews Genetics.

[14]  Jonathan F. Wendel,et al.  Genome evolution in polyploids , 2004, Plant Molecular Biology.

[15]  A. Steinmetz,et al.  Exon shuffling in anther-specific genes from sunflower , 1994, Molecular and General Genetics MGG.

[16]  Manyuan Long,et al.  Duplication-degeneration as a mechanism of gene fission and the origin of new genes in Drosophila species , 2004, Nature Genetics.

[17]  G. Khush.  Origin, dispersal, cultivation and variation of rice , 1997, Plant Molecular Biology.

[18]  K. Holsinger.  The neutral theory of molecular evolution , 2004 .

[19]  Sean R. Eddy,et al.  Pack-MULE transposable elements mediate gene evolution in plants , 2004, Nature.

[20]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[21]  Qihui Zhu,et al.  Phylogenetic relationships among A-genome species of the genus Oryza revealed by intron sequences of four nuclear genes. , 2005, The New phytologist.

[22]  D. Pinkel,et al.  Array comparative genomic hybridization and its applications in cancer , 2005, Nature Genetics.

[23]  Yujun Zhang,et al.  Computational Identification of 69 Retroposons in Arabidopsis1[w] , 2005, Plant Physiology.

[24]  Jun Wang,et al.  High Rate of Chimeric Gene Origination by Retroposition in Plant Genomes[W] , 2006, The Plant Cell Online.

[25]  J. Roman Arguello,et al.  Origination of an X-Linked Testes Chimeric Gene by Illegitimate Recombination in Drosophila , 2006, PLoS genetics.

[26]  M. Long,et al.  A New Retroposed Gene in Drosophila Heterochromatin Detected by Microarray-Based Comparative Genomic Hybridization , 2007, Journal of Molecular Evolution.

[27]  K. H. Wolfe,et al.  Gene duplication, exon gain and neofunctionalization of OEP16-related genes in land plants. , 2006, The Plant journal : for cell and molecular biology.

[28]  Yoav Gilad,et al.  Using DNA microarrays to study natural variation. , 2006, Current opinion in genetics & development.

[29]  Takeshi Itoh,et al.  Rate and polarity of gene fusion and fission in Oryza sativa and Arabidopsis thaliana. , 2007, Molecular biology and evolution.