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Surprisingly, Phyllostachis sequences are only 9% divergent from the copies of maize and Sorghum orthologs which correspond to a 3,3 MY radiation whereas Bamboo and Panicoideae diverged 50 MYa.
In general, only full-length copies of maize, sorghum, rice, and Brachypodium CRs that were flanked by 5 bp target site duplications (TSDs) containing no more than one mismatch were used in this study.
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Conserved Route66 genomic copies of rice, maize and Sorghum were aligned using CLUSTALX [ 55] and modified by hand using SEAVIEW software [ 56].
In terms of the DNA concentration, this indicates that at least 150 genome copies of each transgene maize tested were added per PCR reaction, except in the case of TC1507 and CBH351 maize, where only 7 and 24 DNA copies were present, respectively.
Two helitrons containing hundreds of copies in maize inbred line B73 have been identified [ 13].
We mined 12 additional complete copies of the element from maize and 5 from Sorghum.
For the moment, our working hypothesis is that maize1 gene copies have predominantly retained the ancestral function of the gene in the pre-duplication ancestor of maize, leaving maize2 copies free to potentially adopt new, or less essential functions.
In maize, the P2 nuclear genotype is used as a system for understanding mutations in mtDNA, where abnormal recombination products remarkably increase as the copy number of subgenomic molecules of maize mtDNA increases [ 36].
Only one representative sequence was kept per species and these were aligned with the corresponding regions of maize, rice and Sorghum genomic copies.
The duplication of the two Fie genes resulting from WGD in the progenitor of maize possibly led to four gene copies that were disadvantageous.
Another example of reasonably stable polyploid gene copies comes from a comparative study of the adh1-orthologous regions of maize, sorghum and sugarcane [42].
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