Skip to main content

Advertisement

Table 4 Mapping statistics for sea bass BAC-ES comparatively mapped to the stickleback chromosomes XV to XXI.

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

A stickleback chromosome CHR XV CHR XVI CHRXVII CHRXVIII CHRXIX CHR XX CHR XXI
  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
  genetic linkage group sea bass LG13 LG15 LG1? LG17 LG6 LG16/18? LG18?
B sea bass BAC-contigs 20 (29) 24 (38) 30 (30) 35 (43) 38 (43) 22 (35) 9 (17)
  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)
  % 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%)
  number of BACs in min. tiling path 156 (150) 182 (167) 163 (138) 170 (143) 206 (185) 194 (178) 111 (116)
  paired end aligned consistent BACs 969 (619) 916 (533) 784 (459) 783 (373) 1,004 (628) 1,077 (639) 639 (393)
  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)
C inconsistently aligned same chr. 73 (96) 47 (74) 37 (34) 68 (78) 104 (128) 30 (46) 7 (10)
  potential intra-chr. rearrangements between stickleback and sea bass 10 8 6 12 14 8 2
  intra-chr. rearrangements also found between medaka and stickleback 9 4 4 6 8 6 2
  BAC-contigs with same neighbour in medaka as in stickleback 3 7 4 9 7 3 4
D total annotated genes in ensembl 779 799 698 761 1,037 927 460
  % 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%)
  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.