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Tinospora cordifolia Analysis Summary
Raw Data:
A total of 43,090 denovo assembled transcripts were generated by assembling all the publically available RNASeq data set of Tinospora cordifolia, and used for designing microsatellite markers as well as identification of transcription factors.
Softwares Used:

          1)  Krait v1.3.3

          2)    Primer3 V1.0
Parameters used to predict SSRs
                        A)     Definement of microsatellites (unit size / minimum number of repeats):

                                 Mono= (1/10)

                                     Di-nucleotide= (2/6)

                                     Tri-nucleotide=(3/5)

                                                     Tetra-nucleotide= (4/5)

                                     Penta-nucleotide= (5/5)

                                     Hexa-nucleotide =(6/5)

                        B)    Maximal number of bases interrupting 2 SSRs in a compound microsatellite:  100
Parameters used to design SSR specific primers (Primer3 V1.0) 

                         1. Range of primer length=20-25 bp;

                         2. Annealing temperature=650C; GC content of (40-60%) with optimum of 50%;

                         3. Remaining parameters were kept at the default setting for Primer3 V1.0

Results:
Table1: Microsattelites prediction summary
Total number of assembled transcripts examined 43090
Total size of assembled transcripts sequences (bp) 23463538
Number of SSR containing transcript sequences 4267
Number of sequences containing more than 1 SSR 938
Total number of  Perfect SSRs 5624
Number of Compound SSRs 360
Number of Imperfect SSRs 32551
 
Table2: Category wise distribution of predicted SSRs
SSR Type Number Percentage
Mono-(1) 2958 52.60
Di-(2) 994 17.67
Tri-(3) 1508 26.81
Tetra-(4) 114 2.03
Penta-(5) 37 0.66
Hexa-(6) 13 0.23
Total- 5624 100
 
                                  
Figure 1: Distribution of predicted SSRs in different repeat classes
 
Table 3: Primer3 V1.0 based SSRs specific primer result summary
SSR Type Total Number SSRs with Primer sequence
Di-nucleotide 983
Tri-nucleotide 1423
Tetra-nucleotide 119
Penta-nucleotide 83
Hexa-nucleotide 12
TOTAL 2620
Using Primer3 we successfully synthesized 3 Primer pairs each for 2620 (46.58 %) SSRs motifs predicted in 2116 assembled transcripts
                        
Figure 2: Distribution of designed SSR primers in five repeat classes
The Detailed information of contigs associated with SSR markers is given in the download section click here to download
Ref: Singh, Rakesh, Rajesh Kumar, Ajay Kumar Mahato, Ritu Paliwal, Amit Kumar Singh, Sundeep Kumar, Soma S. Marla, Ashok Kumar, and Nagendra K. Singh. "De novo transcriptome sequencing facilitates genomic resource generation in Tinospora cordifolia." Functional & Integrative Genomics (2016): 1-11.
Copyright © Reg. No. SW-15428/2022 ICAR-National Bureau of Plant Genetic Resources, New Delhi, India.
This work is supported by Indian Council for Agricultural Research, Government of India, New Delhi