Skip to main content

Table 2 Mapping statistics for sea bass BAC-ES comparatively mapped to the stickleback chromosomes I to VII.

From: The European sea bass Dicentrarchus labrax genome puzzle: comparative BAC-mapping and low coverage shotgun sequencing

A

stickleback chromosome

ALL CHR

CHR I

CHR II

CHR III

CHR IV

CHR V

CHR VI

CHR VII

 

stickleback chromosome size [bp]

400,788,495

28,185,914

23,295,652

16,798,506

32,632,948

12,251,397

17,083,675

27,937,443

 

genetic linkage group sea bass

-

LG13

LG5

LG10

LG2/?

LG1

LG11

LG3/LG14

B

sea bass BAC-contigs

588 (816)

34 (58)

28 (44)

24 (29)

42 (62)

16 (28)

24 (36)

43 (65)

 

largest BAC-contig [bp]

8,860,934 (5,034,967)

6,029,661 (4,511,889)

4,235,816 (2,100,554)

3,575,021 (2,455,450)

7,720,774 (3,886,881)

1,931,357 (1,573,884)

8,860,934 (5,034,967)

4,327,197 (2,521,767)

 

% of chr. covered by BAC-contigs

87.0% (78.1%)

84.8% (75.6%)

90.0% (83.6%)

85.5% (76.0%)

86.6% (76.2%)

88.5% (83.4%)

85.3% (77.5%)

89.3% (78.9%)

 

number of BACs in min. tiling path

3,929 (3,629)

271 (257)

227 (221)

161 (144)

313 (283)

121 (118)

162 (147)

281 (266)

 

paired end aligned consistent BACs

20,635 (12,076)

1,465 (802)

1,254 (772)

874 (510)

1,593 (883)

731 (418)

993 (678)

1,486 (849)

 

one end aligned BACs

24,940 (25,845)

1,759 (1,781)

1,399 (1,453)

1,199 (1,196)

2,012 (2,111)

784 (839)

1,052 (1,087)

1,855 (1,940)

C

inconsistently aligned same chr.

1,487 (1,920)

98 (128)

77 (100)

93 (128)

111 (152)

57 (80)

64 (96)

97 (132)

 

potential intra-chr. rearrangements between stickleback and sea bass

214

12

8

17

10

6

9

14

 

intra-chr. rearrangements also found between medaka and stickleback

139

9

5

17

8

2

1

10

 

BAC-contigs with same neighbour in medaka as in stickleback

149

7

4

4

16

4

7

7

D

total annotated genes in ensembl

19,045

1,253

853

923

1,317

733

749

1,311

 

% genes covered by BAC-contigs

85.4% (77.5%)

80.5% (73.9%)

85.2% (78.8%)

86.5% (79.2%)

88.3% (79.3%)

88.4% (83.2%)

78.2% (72.0%)

86.7% (76.1%)

  1. Rows (A) show a summary of the 21 reference chromosomes (stickleback assembly: BROAD S1, Feb 2006) and the known corresponding genetic linkage groups of sea bass according to Chistiakov et al. [30]. Rows (B) summarize consistently mapped BAC-ES, BAC-contigs and reference genome/chromosome coverage of the minimal tiling path. Rows (C) focus on inconsistently mapped BAC-ES, which where further analysed for potential intra-chromosomal rearrangements and compared to the medaka genome as a second reference genome. Rows (D) display the number of annotated genes in stickleback and the percentage of them covered by the sea bass BAC-map. Values in brackets "()" show results for a comparative map that was built by using only BAC-ES data, while all other values represent results of improved mapping using BAC-ES together with whole genome shotgun data.
Back to article page

BMC Genomics

ISSN: 1471-2164

Contact us