Table 2

Repeat composition of the pea genome estimated from genomic abundance of reconstructed contigs

Genome representationa

Copy numbersb



Clusters (contigs)

Total GR

Genome proportion [%]

Copies/1C (domain)

Element length [bp]

Genome proportion [%]


Retroelements

Ty3/gypsy

Ogre-like

77 (632)

6,754,965

20.30

65,000 (RT, PBS)

22,000

33.26

Peabody

5 (42)

703,484

2.11

16,000 (RT)

8,000

2.98

PIGY

23 (70)

361,389

1.09

4,700 (RT)

13,600

1.49

Cyclops

15 (52)

221,925

0.67

2,700 (RT)

12,300

0.77

Ty1/copia

Ps-copia-1/751

6 (14)

690,339

2.07

full-length

8,000 (RT)

8,000

1.49

solo-LTR

9,000

1,400

0.29

SIRE

9 (87)

548,280

1.65

(1.65)

PDR

6 (24)

214,755

0.65

1,100 (RT)

4,000

0.10

Other copia

16 (26)

101,805

0.31

(0.31)

Other RE

17 (111)

878,773

2.64

(2.64)

DNA transposons

MuDR

7 (24)

68,247

0.21

(0.21)

En/Spm

5 (9)

50,845

0.15

(0.15)

Tandem repeats

45S rDNA

1 (6)

348,987

1.05

5,300

8,680

1.07

5S rDNA

1 (3)

13,134

0.04

(0.04)

PisTR-B

1 (7)

147,113

0.44

(0.44)

Other satellites

16 (73)

381,148

1.15

(1.15)

Total :

34.5 %

48.0 %


aGenome proportion of individual groups of repeats was estimated from the sum of genome representation (GR) values of corresponding clusters of contigs.

b Estimates based on genomic copy numbers inferred from the read depth of contigs including conserved sequence domains (RT, reverse transcriptase; PBS, primer binding site). Genome proportion of the repeats was calculated using the length of the complete elements and therefore it is provided only for repeat families with known full-length copies in the pea genome.

Macas et al. BMC Genomics 2007 8:427   doi:10.1186/1471-2164-8-427

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