Skip to main content

Advertisement

Table 3 Difference of expanded and contracted sorghum regions syntenic to sugarcane BACs and gene and repetitive elements content of the expanded/contracted region of sorghum

From: A BAC library of the SP80-3280 sugarcane variety (saccharum sp.) and its inferred microsynteny with the sorghum genome

Chromosome Number of syntenic regions Sum of sugarcane BAC nucleotides (bp) Sum of nucleotides of syntenic sorghum regions (bp) Nucleotide difference between sorghum and sugarcane syntenic regions (bp) Gene density of the sorghum chromosomes (%) Repetitive elements of the sorghum chromosomes (%) Distribution of sugarcane BACs among sorghum chromosomes (%)
Chromosome 1      21.3 43.4 11.5
Expanded regions 2 228,757 438,099 209,342    
Contracted regions 2 246,930 170,629 −76,301    
Chromosome 2      15.1 60.1 16.4
Expanded regions 7 843,489 1,530,484 686,995    
Contracted regions 3 390,747 307,693 −83,054    
Chromosome 3      16.8 58.2 16.4
Expanded regions 3 300,722 649,695 348,973 2.3 12.7  
Contracted regions 5 623,310 501,139 −122,171 16.9 6.5  
Chromosome 4      14.9 56.2 8.2
Expanded regions 2 228,311 542,706 314,395 5.5 15.6  
Contracted regions 1 129,840 60,597 −69,243 28.0 20.0  
Chromosome 5      8.1 65.9 3.3
Expanded regions 1 105,911 192,480 86,569 19.6 59.2  
Contracted regions 1 188,640 93,686 −94,954 13.6 47.8  
Chromosome 6      12.8 66.3 3.3
Expanded regions 0 na na na na na  
Contracted regions 2 247,660 68,939 −178,721 0.0 35.9  
Chromosome 7      9.2 66.2 6.6
Expanded regions 1 44,210 296,520 252,310 6.0 57.8  
Contracted regions 0 na na na na na  
Chromosome 8      9.0 65.6 6.6
Expanded regions 2 266,020 341,742 75,722 0.2 33.2  
Contracted regions 1 125,996 124,114 −1,882 13.1 52.1  
Chromosome 9      11.8 61.6 11.5
Expanded regions 2 221,580 423,004 201,424 27.2 23.5  
Contracted regions 1 114,955 91,453 −23,502 23.5 25.2  
Chromosome 10      12.0 60.9 16.4
Expanded regions 2 184,310 374,313 190,003 8.0 13.9  
Contracted regions 4 502,882 283,520 −219,362 12.2 5.7  
Total   4994270 6490813 1496543    
  1. Number of regions: concordant syntenic regions with either increased or decreased size in sorghum compared to sugarcane.
  2. Sum of sugarcane BAC nucleotides: size of sugarcane BAC in nucleotides as determined by Not I restriction digestion analysis.
  3. Sum of nucleotides corresponding to syntenic sorghum regions: sum of nucleotides of the sorghum region corresponding to syntenic sugarcane BACs.
  4. Nucleotide difference between sorghum and sugarcane syntenic regions: positive values indicate regions that are expanded and negative values indicated regions that are contracted in sorghum as related to sugarcane BACs.
  5. Gene density of the sorghum chromosomes: percentage of gene encoding sequences (bp) in each sorghum chromosome.
  6. Repetitive elements of the sorghum chromosomes: percentage of nucleotides corresponding to repetitive elements in each sorghum chromosome. Distribution of sugarcane BACs among sorghum chromosomes: percentage of concordant syntenic sugarcane BACs positioned in each one of the sorghum chromosome.