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In fact, it is possible that the first two bands (2120 and 1981 kb) and eventually the last band (730 kb) are duplicated, based on their higher intensity, compared with the other bands observed in the gel (Fig. 1).
Among the 5,789 genes encoding the A. thaliana PIN, 883 were found to be singleton, and 3,532 were deemed as duplicated based on similarity searches (the rest of the genes remained unclassified; see Materials and Methods).
2877 WGD-duplicated genes (also known as ohnologs) with available PPI data were obtained from Nakatani et al. [ 27]. 307 genes that were not classified by us as duplicated based on our criteria of BLASTP sequence similarity and alignment length (above) were classified as WGD-duplicate genes based on Nakatani's analysis which includes comparative gene synteny.
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b) We examined centriole duplication 3 days after induction SAS-6 expression, and saw that most cells had a high number of centrioles/centrosomes due to the initial burst of de novo assembly, and more importantly, most of these centrioles could duplicate (based on STIL & centrin doublet staining) regardless of whether they were derived from FL, F131E or DM4.
Excluding unmapped contigs, pericentromeric regions represent 3.4% of genomic sequence, but show an enrichment of 2.4-fold for duplications (p-value < 0.001) and contain 8.1% of all duplicated bases.
Similarly, subtelomeric regions show an enrichment of 1.9-fold (p-value < 0.001) and contain 6.7% of duplicated bases.
The proportion of duplicated bases varied from 1.2%to6.9%9% across different chromosomes as showed in Additional file 2: Figure S3.
In this comparison based on the number of bases, the α-globin cluster again shows the highest conversion frequency, with 75.0% of its duplicated bases involved in conversions.
The total length of these intervals reached 542.6 Mb, amounting to 19.3% of the reference genome, which indicated an excessive content of duplicated bases.
All predicted duplicated bases that overlap these regions were totaled and chi-square tests were used to test the null hypothesis of no enrichment as previously described [ 34].
More than 20% of the duplicated bases in the β-globin, α-globin, and IFN clusters were involved in conversion events at least twice.
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