Table 3.

Analyzed plant genomes in version 9.0 of Phytozome.

Organism	Common name	Version
Arabidopsis thaliana	Thale cress	TAIR version 10 (Swarbreck et al., 2008)
Glycine max	Soybean	US Department of Energy (DOE) Joint Genome Institute (JGI) Soybean (Glycine max) genome project version 1.1 (Schmutz et al., 2010)
Medicago truncatula	Barrel medic	Medicago Genome Sequence Consortium Mt3.5 version 4.0 (Young et al., 2011)
Lotus japonicus	Bird's-foot trefoil	Kazusa DNA Research Institute Lotus japonicus genome assembly build 2.5 (Sato et al., 2008)
Phaseolus vulgaris	Common bean	DOE-JGI Phaseolus genome project version 1.0
Zea mays	Maize	Unfiltered protein coding models from Maizesequence.org release 5b.60 (Schnable et al., 2009)

The gene-calling procedure for each genome is described in detail in the indicated publication of the “Version” column.