Comparison of 11 plant genomes that diverged from a common ancestor 150 300 Mya unraveled 27,135 orthologous gene relationships defining 685 collinear blocks and covering on average 81% of the considered plant genomes, cf. table 1.
Similarly, in comparative studies in grass genomes, which are considered very much in terms of rearranged collinear blocks [ 12], little attention has been paid to the regions of collinearity breakdown.
Same colors represent collinear blocks between genomes.
Collinear blocks within the O. sativa subsp. japonica genome were determined by McScan v8 (http://chibba.agtec.uga.edu/duplication/index/files), the output data was downloaded and searched for presence of lectin genes.
Subsets of multi-MUMs were then used as anchors, and were divided into local collinear blocks.
In order to determine the local collinear blocks (LCB), the SPRING tool [7] was utilized.
First, it finds collinear (synteny) blocks between the two genomes by creating pair-wise alignments and then it generates a global alignment for the entire region that covers the collinear blocks.
As shown in Figure 3a, S. halifaxensis had 10 very large genomic segments or Locally Collinear Blocks (LCB) ranging from 0.26 to 1.09 Mb conserved in S. pealeana.
Alignment of plasmids pCLL and pCP13 (Fig. 7) revealed 16 locally collinear blocks (LCBs) with at least some portion of them found in pCP13.
Surprisingly, this analysis identified regions of homology between pCLL and pCP13, which are graphically displayed as colored locally collinear blocks (LCBs) (Fig. 7).
