A genomic survey of transposable elements in the choanoflagellate Salpingoeca rosetta reveals selection on codon usage

Table 4 Frequency of optimal codons (F_op) in non-domain and domain regions of S. rosetta TE genes

Family	Non-domain F_op	Domain F_op	Significance (Fisher’s Exact Test)^a
LTR Retrotransposon Families
Sroscv1	0.565	0.576	NS
Sroscv2	0.591	0.609	NS
Sroscv3	0.559	0.472	0.002
Sroscv4	0.700	0.684	NS
Sroscv5	0.621	0.619	NS
Srosgyp1	0.684	0.725	NS
Srosgyp2	0.663	0.688	NS
Srospv1	0.593	0.619	NS
Srospv2	0.698	0.783	< 0.001
Srospv3	0.711	0.820	< 0.0001
Srospv4	0.457	0.438	NS
Srospv5	0.531	0.596	< 0.03
Transposon Families
SrosH	0.608	0.636	NS
SrosHar	0.459	0.415	NS
SrosM	0.530	0.456	NS
SrosTig1	0.477	0.548	NS
SrosTig2	0.466	0.519	NS
SrosTm	0.590	0.649	NS

^a P values showing significantly elevated values of F_op in domain regions are highlighted in bold

ISSN: 1759-8753