Table 4 |
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Mapping statistics for sea bass BAC-ES comparatively mapped to the stickleback chromosomes XV to XXI. |
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|
A |
stickleback chromosome |
CHR XV |
CHR XVI |
CHRXVII |
CHRXVIII |
CHRXIX |
CHR XX |
CHR XXI |
|
|
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|
stickleback chromosome size [bp] |
16,198,764 |
18,115,788 |
14,603,141 |
16,282,716 |
20,240,660 |
19,732,071 |
11,717,487 |
|
|
|
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|
genetic linkage group sea bass |
LG13 |
LG15 |
LG1? |
LG17 |
LG6 |
LG16/18? |
LG18? |
|
|
|
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|
B |
sea bass BAC-contigs |
20 (29) |
24 (38) |
30 (30) |
35 (43) |
38 (43) |
22 (35) |
9 (17) |
|
|
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|
largest BAC-contig [bp] |
3,426,120 (1,723,928) |
6,616,511 (2,444,746) |
3,516,936 (2,019,946) |
1,934,982 (1,280,086) |
2,450,075 (2,125,025) |
7,220,725 (2,296,377) |
4,139,228 (2,305,187) |
|
|
|
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|
% of chr. covered by BAC-contigs |
89.3% (82.5%) |
88.4% (79.0%) |
88.5% (78.7%) |
83.6% (70.6%) |
86.6% (78.2%) |
90.3% (82.8%) |
87.4% (83.3%) |
|
|
|
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|
number of BACs in min. tiling path |
156 (150) |
182 (167) |
163 (138) |
170 (143) |
206 (185) |
194 (178) |
111 (116) |
|
|
|
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|
paired end aligned consistent BACs |
969 (619) |
916 (533) |
784 (459) |
783 (373) |
1,004 (628) |
1,077 (639) |
639 (393) |
|
|
|
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|
one end aligned BACs |
1,017 (1,057) |
1,163 (1,162) |
1,110 (1,145) |
989 (1,040) |
1,204 (1,187) |
1,178 (1,183) |
693 (691) |
|
|
|
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|
C |
inconsistently aligned same chr. |
73 (96) |
47 (74) |
37 (34) |
68 (78) |
104 (128) |
30 (46) |
7 (10) |
|
|
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|
potential intra-chr. rearrangements between stickleback and sea bass |
10 |
8 |
6 |
12 |
14 |
8 |
2 |
|
|
|
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|
intra-chr. rearrangements also found between medaka and stickleback |
9 |
4 |
4 |
6 |
8 |
6 |
2 |
|
|
|
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|
BAC-contigs with same neighbour in medaka as in stickleback |
3 |
7 |
4 |
9 |
7 |
3 |
4 |
|
|
|
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|
D |
total annotated genes in ensembl |
779 |
799 |
698 |
761 |
1,037 |
927 |
460 |
|
|
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|
% genes covered by BAC-contigs |
87.9% (84.1%) |
88.5% (80.4%) |
85.5% (77.4%) |
82.7% (69.5%) |
82.5% (75.5%) |
89.5% (85.1%) |
93.9% (86.7%) |
|
|
|
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|
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. |
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|
Kuhl et al. BMC Genomics 2010 11:68 doi:10.1186/1471-2164-11-68 |
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