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.
Highlights
Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species
Because previous Helitron sequences were missing intact coding sequences it was not possible to determine when they were copied from their donor site
From sequence alignments with the two orthologous copies of the maize genome and the copy of the rice genome, it appears that the Helitron-based movement of the paralogous cytidine deaminase (CDA) gene copy occurred about 4.5 mya
Summary
Genetic maps are based on recombination of orthologous gene sequences between different strains of the same species. Gene sequences of closely related plant species as heterologous markers of genetic maps made it possible to align chromosomal regions of these species according to the order of genes conserved through speciation, called orthologs [1]. Several comparative sequence analyses among maize inbred lines have shown that haplotype variability within the same species did differ by transposable element insertions and by the presence of non-allelic gene copies [9,10,11]. Retrotranspositions account for major dissimilarities between aligned regions, more than one-third of the predicted genes (27/ 72) are absent in one of the inbreds (B73 and Mo17) at the loci 9002, 9008 and 9009 [11] In all these cases the inserted genes are incomplete and represent gene fragments except at the z1C1 locus in BSSS53 [10]. While the RAV-like gene in B73 is a gene fragment linked to a transposable element (Xu and Messing, unpublished data), reminiscent of the Pack-MULEs [13], the two genes in BSSS53 appear to have complete open reading frames
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