Skip to main content

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

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

  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
  1. *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.