Subgenome Dominance in an Interspecific Hybrid, Synthetic Allopolyploid, and a 140-Year-Old Naturally Established Neo-Allopolyploid Monkeyflower.
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...These results suggest that the polyploid context and the polyploidization process itself affect the relative expression of homoeologs comparedwith the baseline expression in the progenitor species (13), which has also been observed during the evolution of polyploid cotton (26) and monkeyflower (27)....
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...These results suggest that epigenetic status in gene bodies, as well as upstream and downstream regions, is associated with homoeolog expression bias in polyploid wheat, consistent with results inmonkeyflower showing changes inDNAmethylation upon polyploidization (27)....
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"Subgenome Dominance in an Interspec..." refers methods in this paper
...The Benjamini-Hochberg correction (Benjamini and Hochberg, 1995) was made to correct for multiple testing error for the first test, but not the second, since we were asking whether we were unable to reject H1 in favor of H2....
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70,111 citations
"Subgenome Dominance in an Interspec..." refers methods in this paper
...guttatus genome assembly by TBLASTN (Altschul et al., 1997), as implemented in the TARGeTpipeline (Han et al....
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...The DDE/ D domain alignment profile for each of the five superfamilies (obtained from Yuan and Wessler, 2011) was used as query to search against the M. guttatus genome assembly by TBLASTN (Altschul et al., 1997), as implemented in the TARGeTpipeline (Han et al., 2009)....
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"Subgenome Dominance in an Interspec..." refers methods in this paper
...Codon alignments from CDS were used to reconstruct gene trees using RAxML v.7.3.0 (Stamatakis, 2006) under a GTR+gamma model and 500 bootstrap replicates....
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