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For 1707 (31.90% of hit-producing NTRs) NTRs, the best blast hits were against A. aegypti proteins, suggesting that they may represent paralogs of previously annotated AAEL genes.
Some of these may represent paralogs that were collapsed in the M_zebra_v0 assembly and have been separately assembled in the M_zebra_UMD1 assembly.
We chose to remove these two loci from further analyses because they may represent paralogs, although none of our overall results vary with their inclusion.
For 404 NTRs (52.46% of hit-producing NTRs), the best blast hits were against N. vitripennis proteins, suggesting that they may represent paralogs of previously annotated N. vitripennis genes.
These divergent SMC3 copies in D. pulex and Anopheles may represent paralogs that have gained unique cellular function(s); further taxon sampling across all eukaryotes can address this question.
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Of the novel recA and rpoB homologs identified in the metagenomic data, some likely come from uncharacterized viruses while others may represent ancient paralogs not yet seen in any cultured organism.
Alternatively, some of the Dasypyrum-like sequences may represent divergent paralogs.
These clones represent paralogs of A. thaliana thionins.
Thus we assume that they represent paralogs arisen from a recent duplication.
This suggests that they represent paralogs that have arisen by gene duplications in the Pristionchus lineage.
When this occurs, the symmetrical best hits will actually represent paralogs that have artificially high levels of sequence diversity.
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