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This is the first confirmation by genome-wide analyses using nuclear genes of the three major groups of bilaterians.
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Paralogy is the leading concern when using nuclear genes, especially members of multigene families.
The analyses of population structure using nuclear genes (Fig. 5) suggest some gene flow when the northern and southern ESUs come into contact with each other and the Santa Cruz population.
Zeng, L. et al. Resolution of deep eudicot phylogeny and their temporal diversification using nuclear genes from transcriptomic and genomic datasets.
For our nuclear analyses, we used nuclear genes obtained from GenBank.
Ribosomal candidate genes (5.8SrRNA, 18SrRNA, 28SrRNA, ITS1, and ITS2) were screened through BLAST in G. tridactyla (Glytri) using published nuclear genes of Glycera americana 28SrRNA (EU418864.1), Proceraea cornuta 5.8SrRNA (and12165.1), and G. americana 18SrRNA (EU418856.1) as reference.
using nuclear and mitochondrial genes.
Previous analyses using nuclear-encoded genes have found either conflicting placements of pseudoscorpions depending upon the method of analysis, or less than 50% bootstrap support for the placement of pseudoscorpions [ 32, 33].
In the 2000s, a phylogenetic analyses using nuclear and mitochondrial ribosomal gene sequences helped to clarify the phylogeny of Calostoma.
Hepatic NF-κB activity was determined by measuring both NF-κB-DNA-binding activity using nuclear proteins and the expression of NF-κB target genes.
Annotated nuclear genes of C. variabilis, A. protothecoides46, Helicosporidium sp.21, P. cutis, and P. stagnora were classified into known gene families using TreeFam 930 with an E-value cut-off of 1E-5.
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