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The most frequent functional categories for our data were "Posttranslational modification, protein turnover, chaperones (category symbol O)" and "general function prediction only (R)," which agreed with previous reports [ 21, 26- 28].
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Although the number of pseudogenes is not directly correlated to the number of its active paralogs in a given family, we observed frequent formation of pseudogenes in these functional categories.
The other functional categories are less frequent, except for ten sequences assigned to the COG database function "Energy production and conversion" (see [Additional file 3] for a deeper analysis).
Several functional categories of immunity-related SNP-genes showed frequent polymorphisms in 3'UTRs, and these are often strain-specific.
With this approach, RBHs are interpreted as potential one-to-one orthologs whereas co-orthologs are ignored; this way we are able to look for GO terms overrepresented in the set of sequences that remain unpaired (including possible gene duplications and alternative transcripts) as a means to recognize functional categories that are particularly frequent in the annotation of cassava transcripts.
17,421 COG functional annotations were obtained that were grouped into 24 functional categories (Fig. 3).
The several taxa were placed in functional categories using expert knowledge (Table S4).
We identified 151 differentially expressed proteins and classified them into 11 functional categories.
When fungal OTUs were divided into functional categories, host genotype differences were also detected (Fig. 2b).
Lefebvre, C. Functional Categories in Three Atlantic Creoles: Saramaccan, Haitian and Papiamentu (Benjamins, Amsterdam, the Netherlands, 2015).
We evaluated functional group by placing identified fungi into functional categories (commensal, beneficial and pathogenic) according to the description of fungal endophytes by Hardoim et al.49.49
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