KEGG differences
From Purdue Genomics Database Facility
Victor A. Albert
Plotted are the differences in numbers of gene models (> or = 1) between Selaginella and Physcomitrella annotated for particular KEGG categories, as extracted from the Selaginella JGI home page. The KEGG categories are sorted by increasing difference between Selaginella and Physcomitrella.
It can be seen that the KEGG category flavonoids, stilbene and lignin biosynthesis contains by far the most overrepresented gene models in Selaginella. This can be attributed to greater plant defense capacity and structural integrity of the dominant sporophyte generation.
It is also noteworthy that ubiquinone biosynthesis is among the most overrepresented KEGG categories among Selaginella gene models.
Very few articles in PubMed address ubiquinone biosynthesis in Arabidopsis. One potentially telling report links a gene involved in ubiquinone biosynthesis with embryonic development. Another interesting finding is that tobacco ubiquinones confer tolerance to oxidative stress, for example, as caused by high salinity. It is tempting to speculate that the drastic increase in gene models under this KEGG category may be related to various functions for dealing with oxidative stress in a plant that is both sporophytically dominant (with its major life cycle stage exposed to the environment) rather than gametophytically dominant and endosporic (with gametophytes embedded and protected in spores). Ascorbate peroxidases are also among the important antioxidants in Arabidopsis.
However, a closer look within the ubiquinone synthesis KEGG category reveals that peptide synthases (largest) and methylatransferases (next largest) account for most of the annotated activities. The former are involed in (e.g.) auxin, jasmonate and other signaling pathways, as well as in disease resistance, while the latter is involved in (e.g.) epigenetic gene silencing, herbivore resistance, and cell adhesion during development. Enhanced disease resistance and cell adhesion can certainly be seen as advantageous for an elaborated sporophyte generation.
