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Table 2 GO terms showing the greatest differences in the fraction of genes between mycoheterotrophic species and their photosynthetic relatives

From: RNA-seq highlights parallel and contrasting patterns in the evolution of the nuclear genome of fully mycoheterotrophic plants

Epipogium compared with photosynthetic orchids
GO term Type of GO term Median number of genes with this GO term in Epipogium aphyllum and Epipogium roseum Median number of genes with this GO term in photosynthetic orchids Median ratio of fractions between Epipogium aphyllum and Epipogium roseum versus photosynthetic orchidsa
chlorophyll binding molecular function 0.5 34 0.011
photosynthesis, light harvesting biological process 1 23 0.035
photosystem I cellular compartment 2 38 0.041
plastid thylakoid lumen cellular compartment 1.5 31 0.041
plastid thylakoid membrane cellular compartment 55.5 201 0.20
photosynthesis, light reaction biological process 50 174 0.22
plastid thylakoid cellular compartment 89 275 0.25
photosystem II assembly biological process 28 93 0.25
photosynthesis biological process 125 294 0.35
organelle subcompartment cellular compartment 203.5 403 0.38
Hypopitys monotropa compared with photosynthetic Ericales
GO term Type of GO term Number of genes with this GO term in H. monotropa Median number of genes with this GO term in photosynthetic Ericales Median ratio of fractions between H. monotropa versus photosynthetic Ericalesa
plastid thylakoid membrane cellular compartment 51 247 0.34
photosynthesis, light reaction biological process 51 243 0.37
plastid thylakoid cellular compartment 80 341 0.39
photosynthesis biological process 97 347 0.47
tetrapyrrole binding molecular function 136 395 0.57
plastid cellular compartment 1051 2177 0.81
oxidation-reduction process biological process 1122 2256 0.83
single-organism process biological process 6479 11,495 0.94
  1. GO terms that are similar to each other, such as “plastid thylakoid lumen” and “chloroplast thylakoid lumen”, are combined here
  2. aThe fraction of genes with a specific GO term is the number of genes with that GO term in a species divided by the total number of genes with GO terms in that species. The median ratio of fractions is a measure of the difference in the numbers of genes with a specific GO term between two groups of species, calculated as a median value among all pairwise comparisons in which the first member in a pair comes from the first group, and the second member of the pair comes from the second group