Computational archaeology of the Pristionchus pacificus genome reveals evidence of horizontal gene transfers from insects

Table 1 Accuracies of taxonomic group predictions based on GC-normalized codon usage profiles

Taxonomic group	insect*	bacteria*	amoebozoa*	fungi*	nematode*	plant *
Insects	61.1 ± 0.7	6.8 ± 0.5	0.3 ± 0.1	7 ± 0.4	22.0 ± 0.3	2.8 ± 0.2
Bacteria	8.5 ± 0.2	85.5 ± 0.4	0 ± 0	1.9 ± 0.1	3.6 ± 0.2	0.5 ± 0.1
Amoebozoa	2.2 ± 0.6	1.5 ± 0.3	82.9 ± 1.2	1.7 ± 0.7	10.8 ± 1.7	0.9 ± 0.6
Fungi	10.3 ± 0.6	1.3 ± 0.1	0.2 ± 0.1	71.3 ± 0.7	9.1 ± 0.5	7.9 ± 0.3
Nematodes	12.0 ± 0.4	5.5 ± 0.2	0.5 ± 0.1	7.1 ± 0.2	71.9 ± 0.6	3.0 ± 0.2
Plants	6.8 ± 0.8	2.9 ± 0.4	0.3 ± 0.1	18.1 ± 0.6	13.9 ± 0.9	58.0 ± 1.2

Accuracy was measured using ten randomized data sets including equal number of sequences per species (see Methods). For each taxonomic group (rows), we calculated the mean percentage of predictions for all possible classifications, the "*" indicates the predicted taxonomic group (columns). For instance, while 61.1% of insect genes are correctly recognized as insect sequences based on their codon usage, 22.0% are mistaken as nematode genes.

ISSN: 2730-7182