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

Table 1 Characterisation of the LTR retrotransposon families identified within the S. rosetta genome

Family	Length (bp)	LTR Size	Copy Number (FLE/Solo LTR/ Truncated)	No. of Identical Paralogous Copies	Number of Sequence Reads	Intra-element LTR Identity	LTR Nucleotide Diversity ( π - Total/FLE/Solo)
Sroscv1	5290	243	16 (8/5/3)	10	457	100	0.022	0.006	0.048
Sroscv2	4813	190	7 (4/0/3)	2	243^a	100	0.122	0.122	–
Sroscv3	5165	394	21 (10/10/1)	12	1288	99.2–100	0.019	0.006	0.030
Sroscv4	5965	580	15 (12/1/2)	2	92	99.6	0.039	0.039	–
Sroscv5	6071	408	9 (6/2/1)	2	1591^a	99.5–100	0.026	0.025	–
Srosgyp1	5460	373	9 (6/2/1)	4	197^a	100	0.017	0.003	–
Srosgyp2	5169	385	6 (6/0/0)	4	856	100	0.000	0.000	–
Srospv1	4943	387	14 (11/0/3)	2	327	99.7–100	0.016	0.016	–
Srospv2	5452	554	71 (41/4/26)	17	4211	99.6–100	0.044	0.041	0.077
Srospv3	5680	445	121 (59/14/48)	18	5182	94.2–100	0.083	0.084	0.079
Srospv4	5148	359	4 (1/3/0)	2	48	100	0.001	–	0.002
Srospv5	5088	362	3 (2/0/1)	2	1082	100	0.000	–	–
Srospv6	11,222	168	1 (1/0/0)	0	n/a^b	100	–	–	–

^a Read number based upon edited ORF sequences. ^b n/a: Expression level is not shown for Srospv6, as it is a pseudogene

ISSN: 1759-8753