Furthermore, we performed a comprehensive functional annotation, inferred from sequence alignment (ISA), as well as a gene ontology categorisation inferred from sequence orthology (ISO) of the SSR-containing unigenes.
Analysis of the prophage pan-genome and phage-related genes supported the categorisation of prophages into four clades, where clades 2, 3, and 4 share regions of homogeneity and clade 1 was unique.
In contrast, phylogeny based on the 23S rRNA gene sequence showed no categorisation based on any of the phenotypes.
To gain a comparative insight into the similarities and differences into how organs are built and how plants respond to stress, the transcriptomes of Arabidopsis and rice were compared at the level of gene orthology and functional categorisation.
The Gene Ontology (GO) project [ 60] was used to aid categorisation of genes.
Categorisation of genes affected in leaves and roots of the glu1-2 mutant presented above showed a high number of genes related to stimulus and stress responses.
According to a strict interpretation of our categorisation of genes, on the basis of the 10-10 BLAST cut-off score, the Pomatoceros FMRFamide and mollusc genes represent lophotrochozoan-specific genes, and are counted as such in our classification here.
The 135 k Brassica Exon Array was validated by quantifying transcriptome differences between leaf and root tissue from a reference Brassica rapa line (R-o-18), and categorisation by Gene Ontologies (GO) based on gene orthology with Arabidopsis thaliana.
As there were differences in the functional categorisation of the genes in the FIE-HA+H3K27me3 FIE-HA+H3K27me3ly gene groups, we determined whether these groups of genes differed in the extent to which their expression wandunder PcG regulation.
In addition to noting gross trends of TCS organisation, categorisation of TCS genes allowed analysis of previously unexplored aspects of TCS gene organisation from a multi-genomic perspective.
