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In this framework we assumed that most of the duplicates came from tandem duplication events and that rearrangements occurring within a duplicated segment were independent from the other rearrangement events.
Two pairs of closely positioned singleton genes, one each on chromosome III and IV, and two clustered genes in a duplicated segment on chromosome IV (At4g49260, At4g49380), suggest ancient tandem or local duplication events that have already resulted in substantial gene diversification (<30% identity for each gene pair).
Duplicated segments were analyzed with i-ADHoRe [102], based on the following parameters: gap size of 40 genes, Q value of 0.9, probability cut off of 0.001, and a minimum of 3 homologs to define a duplicated segment.
e. number of pseudogenes being part of a duplicated segment involving other adjacent genes among the first category (a).
The s1 spacer, located between trnQ and nad2, appears to be the result of a duplicated segment.
Our results suggest that when a duplicated segment undergoes a single round of RIP, one copy of it suffers G to A mutations, whereas the other suffers C to T mutations.
Similar(51)
Spacer s3, located between nad3 and trnA, exhibits a partial duplicated segment and a poly-T motif within the first 30 nt.
However, in the N2 genome tbx-30 has an exact duplicate, tbx-42, as part of an inverted duplicated segment; presumably, the loss of a single copy is tolerated.
Contained within the big repeat is a smaller duplicated segment, which could have transposed regulatory elements from F40C5.1 to T24A6.17 (both not hh-related genes).
The only "complex" duplication was found in patient BR1, and consisted of an inverted duplicated segment.
Two groups of tandemly duplicated genes with three genes each were localized on chromosome 4. Incidentally, this region overlapped with an intra-chromosomal duplicated segment suggesting that these six genes probably evolved from a single ancestral gene by a combination of segmental and tandem duplication events.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com