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As our previous segmental duplication analyses detected, 267 Mb of duplicated sequence on Btau_4.0 were considered to be artifacts from a failure to merge high identity alleles on the reference assembly [ 41].
Additionally, the phylogenetic and gene duplication analyses revealed that the BrGRFs contained three triplets, two duplicates, and four singletons.
Duplication analyses were performed based on gene coding sequences (a) and SSR markers (b) in Populus Trichocarpa, and on gene coding sequences (c) and SSR markers (d) in E. guineensis.
This may lend support to the results of phylogenetic and genome duplication analyses.
CDS annotations (identity, sequence, position) were considered for the synteny and duplication analyses described below.
Whole-genome duplication analyses were accomplished as described in Tuskan et al.[ 30].
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Therefore, the whole genome duplication analysed here most probably represents a duplication event that occurred after speciation among the Funariaceae.
We investigated genetic aberrations occurring specifically in JPA not carrying 7q34 duplication analysed by SNP arrays (N=10) and identified recurrent abnormalities (Table 3).
Speciation-duplication analyses in Notung [ 30] identified each of the nodes that represent a divergence between N. viridescens SPF clades as gene duplication events.
Speciation-duplication analyses were done using Notung v2.6 [ 30]. aNewt sexual dimorphic cloacal glands from which pheromones are released are both known as abdominal glands and dorsal cloacal glands [ 2].
Out of 1726 duplications analysed, 287 had the Yates-corrected χ2 test for asymmetry significant after Bonferroni correction (P < 0.05); 451 duplications had asymmetry test surviving false discovery rate correction [ 45] with q < 0.1.
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