It has been reported that Agrobacterium-mediated transformation leads to clean, discrete, low copy, well-defined, unrearranged DNA insertions into the plant genome [ 36, 37].
This is achieved through well-defined mtDNA and single-copy nuclear DNA markers and by taking into account the DNA structural effects on qPCR amplification [ 31].
The phylogenetic tree of MIBs of humans, great apes, and macaques depicts the high level of divergence of eight well-defined lineages of MIB copies in macaques, which are well supported by posterior probability values (PPV) (0.63 to 1).
Details of data and refinement statistics are given in Table 2. Overall, for all three complexes, the electron density 2Fo-Fc maps were continuous and well-defined over all four copies in the asymmetric units (data not shown).
The phylogenetic tree from concatenated DNA sequences of introns 3 and 6 showed two different well-defined clusters, one for each duplicated gene copy, suggesting the independent evolution of RPS4Y1 and RPS4Y2 after the duplication event.
The rest of the eukaryotic ICLs, i.e., those from plants, fungi, and the ciliate Tetrahymena, form a well-defined clade with one of the two copies of the ICL gene from Mycobacteria and Anaeromyxobacter dehalogenans.
To organize the duplications into tractable units, intron-exon structure and well-defined duplication boundaries were used to define 78 duplicated modules (minimally shared evolutionary segments) with 157 copies on chromosome 22.
We confirmed that the repeat element has well-defined boundaries by aligning the 13 full-length copies and 60 bp of their flanking sequence (Fig. 1a).
An average of 110 (50 to 200) well-defined nuclei was analyzed by scoring the number of single copy 13q34 and 13q12.11 signals.
The TP53 gene is a well-defined tumor suppressor gene and is mutated and targeted by DNA copy number loss at a low frequency in a range of B-cell lymphomas.
