Simple Sequence Repeats (SSR) in TGB

      Using a Perl Script, SSRs were identified in the sequences of expressed sequence tags (ESTs) and original reads sequences, which were downloaded from PlantGDB and TGI, respectively. TGB desiged primers to amplify these SSRs using ePrimer3 program and tested by e-PCR in all tobacco sequences.

SSR Methodology

     The flowchart of developing tobacco SSR markers.

SSR Summary Statistics

 

Species Type Numebrs of SSRs identified Nubmer of SSR-containing sequences Nubmer of sequences containing >1 SSR Number of SSRs with Unit 2 Number of SSRs with Unit 3 Number of SSRs with Unit4 Number of SSRs with Unit 5 Number of SSRs with Unit 6 Number of SSRs with Unit 7
N. tabacum Original reads 66,297 66,297 5,841 1,078 876 0 9 2,864 61,455
N. benthamiana EST 1,524 1,420 177 1,142 160 13 8 139 62
N. sylvestris EST 81 80 7 65 7 1 0 5 3
N. tabacum EST 8,712 8,222 802 6,486 729 97 73 751 571
Nicotiana langsdorffii x Nicotiana sanderae EST 234 230 8 194 21 1 2 9 7

 

Query EST-SSR Database

     The EST-SSRs can be searched by ID, PlantGDB ID, motif and resource.

Query Genomic-SSR Database

     The Genomic-SSRs can be searched by ID, Genome ID and motif.

SSRs Development

     This tool finds all perfect simple sequence repeats and develops SSR markers based on the nucleic acid sequences submitted by users.

SSR Downloads

     All of the data in our SSR database are freely available in this website.

 

 

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