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Genomic SSRs (G. hirsutum)

  A novel approach of gene-enrichment of complex plant genome, well known as Hypomethylated partial restriction (HMPR), has been applied for six diverse genotypes of G. hirsutum to construct six specific HMPR librairies by using independent partial digestions with methylation-sensitive restriction enzymes HpaII (5′-CCGG-3′) and ClaI (5′-ATCGAT-3′). All six genotypic specific HMPR libraries were sequenced using Genome Sequencer FLX 454 (Roche) and assembled within genotypes and super- assembled among six genotypes to eliminate the common sequences. All the assembled 40,95,129 unigenes (contigs and singletons) were explored with high stringency criteria for identifying a total of 1,64,189 SSRs. Among all the unit size of different repeat type, DNR stood with maximum frequency (1,16,982) followed by TNR (21,795) and MNR (18,706). Out of 1,45,483 SSRs (excluding MNRs), 56,142 SSRs were found to be successful in primer designing in which 47,093 SSRs were found to be novel against Cotton Marker Database (CMD).
All the Novel SSRs have been submitted to NCBI GenBank under GenBank accession numbers: JX576804-JX623896.
  Details of G. hirsutum genomic SSRs from genic-enriched sequencing    
Details of identified SSRs   
Total sequences examined  4095128
Total SSRs identified  148930
Total SSR containing sequences  135365
Sequences used for primer designing (excluding MNRs)  130223
SSRs  with successful primer designing  56142
Numer of novel SSRs 47093
Unit size of different repeat type No. of SSRs
MNRs (≥10) 12408
DNRs (≥5) 109421
TNRs (≥5) 20700
TtNRs (≥5) 3941
PNRs (≥5) 1583
HNRs (≥5) 877

Frequency details of various types of Genomic SSRs repeat motifs