Table 1 Assembly and annotation of the cheetah genome

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