Question marks were used to represent missing sequences.
Missing sequences between consecutive contigs are represented by segments of ambiguous bases, denoted as Ns, the lengths of estimated gap sizes.
These clones represent either missing sequences from the P. marneffei genome project or contaminating clones in the library.
The total length of singletons was another 36.5 Mb, suggesting that only a modest proportion of these sequences represent unique Douglas-fir transcripts (i.e., missing sequences from already identified genes or unsampled genes).
There are still some missing sequences, which will probably never be rediscovered.
Some segments could not be aligned in all four species, primarily because they represent new sequences recently inserted into the Fg genome, ancestral sequences deleted in one of the other species, or missing sequences in one of the draft genomes.
Interestingly, of the eight genes that we annotated in two sequences identified as the missing sequences of the Williams 82 genome assembly in our previous report, seven had >85% similarity in these 343 genes and four were identical in these 343 genes, indicating that many of the unmapped genes represent genes from missing sequences in the Williams 82 genome assembly.
Deletions or missing sequences are marked with "*".
Large gaps and hyper variable sites were removed from the alignments; the same methodology was applied to gaps at the beginning and end of the alignment, which represent missing sequence data.
These regions of sequence divergence may represent missing sequence in contig gaps, but in some cases, these regions are populated with vsp genes, ankyrin repeat-containing genes, or members of other gene families where sequence divergence is common among family members (data not shown).
