Table 4.

Taxonomic distribution of unigene blastx hits in the nr database

	Best blastx hit		Lowest common ancestor for blastx hits
Taxonomic category	Number of unigenes	Percent of unigenes with hits	Number of unigenes	Percent of Unigenes with hits
Eukaryotes	33,776	97.2%	32,059	92.3%
Green plants	33,406	96.2%	31,373	90.3%
"Green algae"	175	0.5%	78	0.2%
Land plants	33,231	95.7%	30,822	88.7%
"Bryophytes"	394	1.1%	2,197	6.3%
Vascular plants	32,837	94.5%	16,731	48.2%
Lycophytes	74	0.2%	13	0.0%
Ferns	928	2.7%	435	1.3%
Seed plants	31,835	91.6%	16,015	46.1%
Gymnosperms	8,000	23.0%	866	2.5%
Angiosperms	23,835	68.6%	10,572	30.4%
Animals	288	0.8%	63	0.2%
Fungi	0	0.0%	4	0.0%
Other eukaryotes	77	0.2%	12	0.0%
Bacteria	22	0.1%	91	0.3%
Artificial sequences, hits don't pass threshold, or taxon not assigned	20	0.1%	216	0.6%

Unigenes were searched in the NCBI nr protien database using blastx with an e-value threshold of 1e-10, keeping the best ten hits. Of the 56,256 unigenes, 34,740 (61.8%) had a positive hit. The lowest common ancestor (LCA) assignment for a sequence was calculated using the LCA algorithm implemented in MEGAN v3.9 [61] based on at least three blastx hits with a bitscore greater than 75 and within 10% of the best bitscore. Note: the predicted proteins from Selaginella moellendorffii are not currently included in the nr database and thus are not reflected in these results.