Table 2

Summary of elements in ten annotated pine BACs, as identified by MAKER (white background) and through additional repeat analyses performed in this study (shaded background).

BAC3

BAC12

BAC15

BAC17

BAC19

BAC20

BAC21

BAC31

BAC37

BAC40

ALL


No. dicot-like genes

0

2

2

2

1

1

2

1

0

7

18

Dicot-like gene content

0

3.0%

4.7%

4.5%

3.7%

2.5%

2.8%

1.5%

-

6.5%

2.6%

No. monocot-like genes

0

2

2

1

1

1

2

1

0

8

18

Monocot-like genes content

0

20%

3.9%

3.7%

11.3%

2.5%

1.9%

1.5%

-

5.8%

4.2%


TRANSPOSONS

72

46

31

73

47

51

64

79

81

55

599

DNA transposons

23

11

11

19

19

15

28

22

24

18

190

ERVs

4

2

2

6

1

1

2

3

0

6

27

Non-LTR retroelement

7

13

6

18

12

16

7

28

18

7

132

LTR retrotransposons

38

20

12

30

15

19

27

26

39

24

250

Gypsy-like

26

7

9

17

6

14

15

13

26

10

143

    Named elements*

    4

    1

    2

    1

    1

    1

    1

    1

    1

    1

    14

Copia-like

17

3

3

13

6

4

12

10

11

13

92

    Named elements*

    1

    0

    1

    2

    1

    1

    0

    2

    2

    0

    10


INTEGRATED VIRUSES

0

0

1

0

0

0

0

1

0

1

3

OTHER REPBASE

0

0

0

1

0

2

2

1

1

1

8

SIMPLE REPEATS

16

10

4

9

12

2

22

18

41

18

152


TOTAL NO. REPBASE HITS

88

56

36

83

59

55

88

99

123

75

762

Similar to Repbase or RM

18%

12%

12%

15%

17%

19%

12%

17%

15%

9%

17%


Tandem repeats/minisats**

13

11

10

14

23

14

22

45

21

41

214

Direct rpts/potential LTRs**

40

12

10

10

4

6

12

24

27

16

161

Putative ORF elements**

11

5

3

8

5

6

8

3

14

7

70


NO. ADD'L REP. ELEMENTS

64

28

23

32

32

26

42

72

62

64

445

New Repetitive Content

72%

54%

50%

59%

34%

75%

44%

93%

59%

38%

63%


Repetitive content***

at 75% threshold (similarity)

81%

83%

80%

82%

70%

86%

76%

85%

75%

82%

80%

Repetitive content***

at 99% threshold (identity)

25%

21%

22%

24%

15%

35%

19%

30%

15%

29%

24%


*The occurrence of novel gypsy-like and copia-like elements (underlined) was manually examined as described in the text.

**See Methods for a description of the discovery of putative ORF elements, tandem repeats and direct repeats.

***The percentage of sites in each BAC assembly that aligned with one or more WGS reads at thresholds of 75% and 99% identity.

Kovach et al. BMC Genomics 2010 11:420   doi:10.1186/1471-2164-11-420

Open Data