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Therefore because in Phaeodactylum the average scaffold sizes are larger, it should be easier to detect larger duplicated blocks.
The differential size of Esmeraldo compared to CL Brener results from a larger non-coding region with larger duplicated conserved elements within the variable region, while coding region size is comparable.
The breakpoint identified by PacBio-LITS in Figure 3b suggests a similar tandem arrangement for the larger duplicated segment, resulting in a dup-trip-dup structure with an internal triplication on one of the duplicated segments.
In this respect, we can compare the distribution of 2HOM and 3HOM blocks between duplicated and non-duplicated genomes, trying to reduce the effect of genome rearrangements and the breaking up of larger duplicated blocks.
(ii) The conserved orientation of the blocks relative to the centromeres [ 1] indicates that they were formed from larger duplicated blocks (i.e. duplicated whole chromosomes) by reciprocal translocation.
Note that these pseudogenes are not located in subtelomeric regions and are not part of larger duplicated regions including other genes.
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(iv) The duplicated genes of nine out of the ten largest duplicated segments comprised equivalent Ks distributions and gene retention rates suggesting a common origin.
Accordingly, the respective medaka chromosomes 1 and 18 have been shown to contain large duplicated segments having been formed from a same protochromosome by the FSGD [ 32].
This large duplicated 38 genes with known functions and several partial exons, including three exons of nad1, three exons of nad2, and three exons of nad5.
(ii) Synteny between barley and rice involved the largest duplicated rice regions and for at least seven of these paralogous relationship in barley could be resolved to segments that were orthologous to duplicated regions in the ancestral grass genome progenitor.
Seven out of the 10 largest duplicated segments in rice shared synteny with barley and thus seven AD's could be identified (AD_1 to AD_7, Figure 3, Table S4 of Additional file 1).
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