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

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

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

Number of regions: concordant syntenic regions with either increased or decreased size in sorghum compared to sugarcane.
Sum of sugarcane BAC nucleotides: size of sugarcane BAC in nucleotides as determined by Not I restriction digestion analysis.
Sum of nucleotides corresponding to syntenic sorghum regions: sum of nucleotides of the sorghum region corresponding to syntenic sugarcane BACs.
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.
Gene density of the sorghum chromosomes: percentage of gene encoding sequences (bp) in each sorghum chromosome.
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.

ISSN: 1756-0500