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Table 5 Comparative sequence analysis of Upland cotton BESs with the D genome sequence of G. raimondii (DOE Joint Genome Institute, Cotton D V1.0, http://http://www.phytozome.net/cotton.php )

From: Construction of a plant-transformation-competent BIBAC library and genome sequence analysis of polyploid Upland cotton (Gossypium hirsutumL.)

Inquired upland cotton BESs Criteria of the analysis Sequence similarity
  Continuous MinMatch (bp) 100 100 100 100 100 100
All AD-subgenome BESs Sequence identity (%) 100 95 90 80 70 60
(No. of BESs = 9,711; total sequence length = 3,842,009 bp) No. of BESs aligned 57 4,587 6,588 7,118 7,257 7,277
  % of BESs aligned 0.59 47.24 67.84 73.30 74.73 74.94
  Total sequence length of BESs aligned to the raimondii sequence (bp) 15,539 1,367,385 1,960,413 2,048,311 1,996,820 1,975,511
  % of sequence length of BESs aligned to the raimondii sequence 0.41 35.59 51.10 53.31 51.95 51.42
  Continuous MinMatch (bp) 100 100 100 100 100 100
A-subgenome-specific BESs Sequence identity (%) 100 95 90 80 70 60
(No. of BESs = 418; total sequence length = 169,533 bp) No. of BESs aligned 7 205 294 310 317 317
  % of BESs aligned 1.67 49.04 70.33 74.16 75.84 75.84
  Continuous MinMatch (bp) 100 100 100 100 100 100
D-subgenome-specific BESs Sequence identity (%) 100 95 90 80 70 60
(No. of BESs = 184; total sequence length = 71,410 bp) No. of BESs aligned 1 88 128 136 139 139
  % of BESs aligned 0.54 47.83 69.57 73.91 75.54 75.54