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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