The sum of gaps covered by the clones with unpaired BES in both pools was 306, which was ∼1.8 times more than the sum of gaps spanned when MTPs were picked in the larger pool with all the three BAC libraries.
Attempts to activate this BES in two independent clones were unsuccessful, suggesting that this mini-BES may not be functional.
BAC end sequences (BES) in this physical map were masked with RepeatMasker v 3.2.7 [28], using a custom database which integrates repeats from Repbase [29] and plant repeat databases [30] and RetrOryza [31].
It is possible that the MGA7 centromere is located at the 10.65 Mb contig gap (Additional file 3: Table S3), although we did not observe multiple repetitive BES in this region as is usually the case adjacent to centromeres.
It remains possible that the MGA25 centromere is close to 3.1 Mb, the break between the two contigs in our map (Additional file 3: Table S3), but we did not observe the pattern of repetitive BES in this region that is typically found near centromeres.
They were homologous to a total of 5,910 BES in the physical map.
