ArticleBMC genetics2006
Maize haplotype with a helitron-amplified cytidine deaminase gene copy.
Article in BMC genetics, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 49 citations in OpenAlex.
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- Genome-wide association analysis reveals new targets for carotenoid biofortification in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Article
- Mining hidden polymorphic sequence motifs from divergent plantMobile genetic elements · 2014Article
- Rolling-circle transposons catalyze genomic innovation in a mammalian lineage.Genome biology and evolution · 2014Article
- HelitronScanner uncovers a large overlooked cache of Helitron transposons in many plant genomes.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Transposable elements: powerful contributors to angiosperm evolution and diversity.Genome biology and evolution · 2013Article
- Article
- Structural characterization of helitrons and their stepwise capturing of gene fragments in the maize genome.BMC genomics · 2011Article
- Differential gene expression and epiregulation of alpha zein gene copies in maize haplotypes.PLoS genetics · 2011Article
- Pervasive horizontal transfer of rolling-circle transposons among animals.Genome biology and evolution · 2010Article
- The polychromatic Helitron landscape of the maize genome.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Distribution, diversity, evolution, and survival of Helitrons in the maize genome.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Amplification of prolamin storage protein genes in different subfamilies of the Poaceae.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2009Article
- Structure-based discovery and description of plant and animal Helitrons.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Synergy of two reference genomes for the grass family.Plant physiology · 2009Article
- Helitron mediated amplification of cytochrome P450 monooxygenase gene in maize.Plant molecular biology · 2008Article
- Transposable elements in Coffea (Gentianales: Rubiacea) transcripts and their role in the origin of protein diversity in flowering plants.Molecular genetics and genomics : MGG · 2008Article
- Analysis of EST sequences suggests recent origin of allotetraploid colonial and creeping bentgrasses.Molecular genetics and genomics : MGG · 2007Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundGenetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Therefore, it was unexpected to find extensive non-collinearity of genes between different inbred strains of maize. Interestingly, disruption of gene collinearity can be caused among others by a rolling circle-type copy and paste mechanism facilitated by Helitrons. However, understanding the role of this type of gene amplification has been hampered by the lack of finding intact gene sequences within Helitrons.
resultsBy aligning two haplotypes of the z1C1 locus of maize we found a Helitron that contains two genes, one encoding a putative cytidine deaminase and one a hypothetical protein with part of a 40S ribosomal protein. The cytidine deaminase gene, called ZmCDA3, has been copied from the ZmCDA1 gene on maize chromosome 7 about 4.5 million years ago (mya) after maize was formed by whole-genome duplication from two progenitors. Inbred lines contain gene copies of both progenitors, the ZmCDA1 and ZmCDA2 genes. Both genes diverged when the progenitors of maize split and are derived from the same progenitor as the rice OsCDA1 gene. The ZmCDA1 and ZmCDA2 genes are both transcribed in leaf and seed tissue, but transcripts of the paralogous ZmCDA3 gene have not been found yet. Based on their protein structure the maize CDA genes encode a nucleoside deaminase that is found in bacterial systems and is distinct from the mammalian RNA and/or DNA modifying enzymes.
conclusionThe conservation of a paralogous gene sequence encoding a cytidine deaminase gene over 4.5 million years suggests that Helitrons could add functional gene sequences to new chromosomal positions and thereby create new haplotypes. However, the function of such paralogous gene copies cannot be essential because they are not present in all maize strains. However, it is interesting to note that maize hybrids can outperform their inbred parents. Therefore, certain haplotypes may function only in combination with other haplotypes or under specialized environmental conditions.
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