Skip to main content
. 2012 Jun 21;8(6):e1002777. doi: 10.1371/journal.pgen.1002777

Table 1. Characterization of satellite DNA families identified in the pea.

Family1 ChIP enrichment2 Genome proportion (%/Mbp)3 Monomer size4 AT content Localization on chromosomes5
1 2 3 4 5 6 7
PisTR-B 20.5 1.374/59.09 a 50 0.72 T T C C, T C,P T T
TR-1 51.7 0.021/0.91 b 867 0.67 C - C, T C - - -
TR-6 59.3 0.011/0.49 b 245 0.76 - - - - C - -
TR-7 49.7 0.135/5.82 b 164 0.73 C - - - - - -
TR-10 76.3 0.01/0.43 a 659 0.74 - - - C, P - - -
TR-11 74.9 0.103/4.44 b 510 0.76 C C - - C C C
TR-12 5.4 0.006/0.29 a 120 0.69 I P, I I C, I I I I
TR-18 82.5 0.013/0.57 b 1644 0.74 - - C - - - -
TR-19 65.9 0.033/1.43 b 2094 0.77 C - - - C - -
TR-20 50.7 0.004/0.19 b 867 0.76 - - - - - - C
TR-21 44.0 0.006/0.24 b 642 0.73 - - - - - C -
TR-22 102.9 0.004/0.17 b 881 0.76 - - - - - C -
TR-23 10.7 0.002/0.09 b 1813 0.69 - - - - - C -
TR-2 0.6 0.207/8.92 a 440 0.68 - P - - P P -
TR-3 0.3 0.058/2.48 a 82 0.79 - - P I - - -
TR-4 0.6 0.200/8.61 a 172 0.67 - - - - - P -
TR-5 1.1 0.151/6.51 a 54 0.65 - P - - - - -
TR-9 0.4 0.009/0.37 a 189 0.79 T T - - - - T
TR-17 0.5 0.012/0.52 a 191 0.74 - - - - - - I
1

Satellite DNA families which are not at all associated with CenH3 are included in the bottom part of the table, starting from TR-2.

2

ChIP enrichment values were calculated using the top one thousand most repetitive clusters build from 2 million randomly selected reads (Figure S2A). The only exceptions included TR21 and TR-22 which were not represented within this data set. Their enrichment values were therefore calculated from clusters build from ChIP-enriched reads.

3

Genome proportion was estimated as a proportion of reads belonging to a given repeat family to the total number of analyzed reads. The table shows the greater estimate of those calculated from either the top one thousand most repetitive clusters (a) or clusters build from all ChIP-enriched reads (b). The total size of the repeats was calculated from the genome proportion assuming that the genome size of the pea is 4 300 Mbp.

4

Monomer sizes were estimated based on contigs assembled from clustered reads and confirmed by sequencing PCR products amplified from genomic DNA.

5

C – centromeric (associated with CenH3), P – pericentromeric (located in or adjacent to primary constriction but not associated with CenH3), I – intercalary, T – (sub-)telomeric.