High tandem repeat content in the genome of the short-lived annual fish Nothobranchius furzeri: a new vertebrate model for aging research

Table 2 G+C and repeat content of N. furzeri, N. kunthae, tetraodon, stickleback, medaka, and zebrafish

	N. furzeri*		N. kunthae ^†	Tetraodon^‡	Stickle back^‡	Medaka^‡	Zebrafish^‡
	GRZ	MZM- 0403
G+C content of samples (%)	44.9	44.3	44.9	46.6 ± 0.2	44.6 ± 0.1	40.5 ± 0.1	36.6 ± 0.0
Genome-wide^§ (%)	NA	NA	NA	46.4	44.6	40.5	36.6
Repeat content of samples (%)	45.3	45.1	45.1	06.9 ± 0.4	6.6 ± 0.3	15.3 ± 0.6	40.4 ± 0.4
Genome-wide^¶ (%)	NA	NA	NA	5.4	NA	17.5	NA
Tandem repeats (%)	20.6	20.6	10.6	03.6 ± 0.3	2.1 ± 0.2	1.7 ± 0.2	5.0 ± 0.2
Microsatellites (%)	0.9	0.8	1.1	01.1 ± 0.1	0.8 ± 0.1	0.2 ± 0.0	2.0 ± 0.1
Most abundant^¥, unit size (bp)	77	77	31	10	317	20	32
Content (%)	9.5	8.3	1.2	0.7	0.1	0.1	0.1
Interspersed repeats (%)	24.7	24.5	34.5	03.4 ± 0.3	4.5 ± 0.4	13.6 ± 0.6	35.4 ± 0.4
Known repeats (%)	8.9	6.9	09.0	3.1 ± 0.2	3.6 ± 0.2	7.0 ± 0.4	30.6 ± 0.2
Non-LTR retrotransposons	5.2	5.1	07.3	1.2 ± 0.2	1.4 ± 0.3	2.8 ± 0.2	5.8 ± 0.2
LTR retrotransposons	1.4	0.8	01.0	0.2 ± 0.1	0.6 ± 0.1	0.6 ± 0.1	2.3 ± 0.2
DNA transposons	1.7	1.3	01.4	0.6 ± 0.1	0.7 ± 0.1	3.2 ± 0.3	20.9 ± 0.3
Unclassified repeats (%)	15.8	17.6	25.5	0.3 ± 0.1	0.9 ± 0.2	6.6 ± 0.4	4.8 ± 0.3

*The 5.4 Mb genomic sample of strains GRZ and MZM-0403 generated by Sanger sequencing representing approximately 0.3-0.5% of the N. furzeri genome. ^†The 5.4 Mb genomic sample of closely related species N. kunthae. ^‡Mean and standard deviation of ten samples of random genomic sequence sets with each set representing 0.4% of the respective genome. ^§Calculations based on respective genome reference assemblies at Ensembl [21]. ^¶According to Roest Crollius et al. for tetraodon [31], and Kasahara et al. for medaka [20]. ^¥Microsatellites excluded; value for concatenation of ten random sequence sets of tetraodon, stickleback, medaka, and zebrafish, respectively. LTR, long terminal repeat; NA, not available.

ISSN: 1474-760X