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Table 2 Characteristics of ploidy among the three groups of contigs with BESs.

From: Re-annotation of the physical map of Glycine max for polyploid-like regions by BAC end sequence driven whole genome shotgun read assembly

  Diploid-like Tetraploid-like Octaploid-like
Number of sequencesa 20,548 1,070 3,506
Mean number of homeologsb detected at 90% identity 1.5 4.5 8.4
Mean number of homeologs detected at 95% identity 1.3 2.4 4.1
Mean number of homeologs detected at 98% identity 1.2 2.1 2.6
Mean number of homeologs detected at 99% identity 1.1 1.9 2.3
  1. Megablast searches and SNP analysis were used to identify the mean number of homeologous groups of sequences above three identity percentages. Most BES from ctgs 1–3500 showed matches to regions that were single copy, however a significant number of regions from contigs formed from 2 or 4 coalesced regions could be detected at 90, 98 and even 99% sequence identity.
  2. a Two hundred sequences were selected from these groups for visual scoring of the BLAST searches.
  3. b The BAC libraries were each constructed from DNA derived from twenty five different seedlings of cultivar Forrest, bulked after single pod selection at F2:5 from F2:6 to F2:13, but otherwise inbred. Therefore, less than 7% heterogeneity should have remained from 'Dyer' and 'Bragg' the parents of Forrest.