Figure 1. Maize B73 refgen version 1 (x-axis) and version 2 (y-axis). Version 1 has gene models and version 2 is using only genomic sequence. Syntenic pairs (dots) are colored green and blue if in the same or opposite orientation respectively. Analysis can be regenerated at http://genomevolution.org/r/4dq
Figure 2. Syntenic dotplot of maize B73 chromosome 3 between refgen version 1 and version 2. Syntenic gene-pairs (dots) are colored green and blue if in the same or opposite orientation respectively. Note the large inversion near the middle (blue line) and many smaller inversion (blue dots). Results can be regenerated by visiting the master dotplot (http://genomevolution.org/r/4dq) and clicking on the chromosome 3 versus chromosome 3 comparison.Figure 3. GEvo analysis of 1MB of chromosome 3 from maize between refgen version 1 and 2. Version 1 has gene models and non-CDS sequences masked (purple). Note the sets of genes that have been reoriented in version 2. These show up where regions of sequence similarity (pink blocks) are drawn below the dashed line in both panels. Results can be regenerated at http://genomevolution.org/r/4du
These analyses compare the genomic sequence assembled of maize B73 refgen versions 1 and 2. Maize was sequenced bac by bac, and bacs were chosen that tile across all of maize's chromosomes. This means that the relative order of most bacs was correctly determined between and within a chromosome. However, the sequences within a bac were often unordered, and the position of contig sequences within a bac relative to one another is not necessarily correct. Therefore version 1 of maize contained many localized misassemblies. Version 2 of maize aimed to correct many of these errors.
To determine the extent of these corrected errors, syntenic dotplots can be generated between two different versions of a genome. SynMap makes these comparisons easy to perform and provides a variety of visualization options to help identify assembly differences. Figure 1 shows a syntenic dotplot between maize genome assemblies refgen v1 and v2. Each
