Table 1 Assembly and annotation of the cheetah genome
From: Genomic legacy of the African cheetah, Acinonyx jubatus
| Number | Feature | Size | Source | |
|---|---|---|---|---|
| Genome sequence and assembly | 7 cheetahs | |||
| 1 | A. jubatus raineyii (Tanzania) | 3 cheetahs | 75 × reference | Table S2 |
| 2 | A. jubatus jubatus (Namibia) | 4 cheetahs | 5 × resequencing | Table S2 |
| 3 | SOAP deNovo assembly | Tables S1, S4 | ||
| 4 | Assisted assembly with domestic cat Fca-6.2 | Fca-6.2 framework anchors: | Table S5 | |
| a. Radiation Hybrid map | 3000 markers | |||
| b. Linkage map | 60,000 SNVs | |||
| 5 | Estimated genome size (assembly and 17-mer) | 2.375–2.395 Gb | Table S3 | |
| 6 | N50 contigs | 28.2 kbp | Table S4 | |
| 7 | N50 scaffolds | 3.1 Mb | Table S4 | |
| 8 | Average GC content | 0.475 | Figure S3 | |
| Annotation | ||||
| 9 | Coding genes | 20,343 genes | 601.2 Mb | Table S10 |
| 10 | Non-coding RNA 200,045 loci | 17 Mb | Table S11 | |
| a. 43,878 microRNA | 4.41 Mb | Table S11 | ||
| b. 1,605 small nuclear RNA | 186 kbp | Table S11 | ||
| c. 154,031 transport RNA | 12.7 Mb | Table S11 | ||
| d. 531 ribosomal RNA | 85 kbp | Table S11 | ||
| 11 | Single nucleotide variants (SNVs) | 1,820,419 loci | Tables S15–S20 | |
| 12 | Repetitive elements | Interspersed repeats | 746 Mb | Tables S6, S7 |
| 39.48 % of cheetah genome | Tandem repeats | 51.2 Mb | Table S8 | |
| Complex tandem repeats | 2.04 Mb | Table S9 | ||
| 3,126 loci | ||||
| Microsatellites | 23.47 Mb | Table S8 | ||
| 487,898 loci | ||||
| 13 | Genomic rearrangements of cheetah vs domestic cat | 93 Mb | Figures S5, S6 | |
| Tables S13, S14 | ||||
| 14 | Nuclear mitochondrial segments | 105.6 kbp | Table S12 | |
| 15 | Positively selected genes | 946 genes | Datasheet S5 | |
| 16 | GARfield Genome Browser | http://garfield.dobzhanskycenter.org | ||