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Andrographis paniculata Transcriptome Analysis Summary |
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Raw Data used for the genic-SSR mining and primer
designing
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De novo meta-transcriptome assembly using our in-house RNA-Seq data of
A. paniculata generated through
Roche-454 GS-FLX platform (SRA Acc. No. SRR719255), and other publically
available RNA-Seq data of the same species and tissue generated through
different sequencing platforms including Illumina (SRA Acc. No. SRR1519324,
SRR12791806, SRR12791807, SRR1292497), and semiconductor-based technology Ion
Torrent
(SRA Acc. No. SRR8500525) generates a total of 98,514 non-redundant transcripts.
These 98,514 non redundant transcripts further used for the identification of
microsatellite markers, their primer pairs, and transcription factors.
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Identification of Microsatellite markers (SSRs)
Microsatellite marker (SSR) identification has been performed using Krait
v1.3.3 software with the parameters: six repeat units for di-nucleotide, and
five repeat units for tri-, tetra-, penta-, and hexa-nucleotide repeats and
number of bases interrupting two SSRs in a compound microsatellite to be 100 bp.
Table 1. Summary statistics of the perfect SSRs predicted using
the Krait v1.3.3 software.
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Item
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Description
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Number
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Number of perfect SSRs
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Counts
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37,814
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Total length of perfect SSRs
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Bp
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651,825
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Average length of perfect SSRs
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Total length (bp)/No. of SSRs
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17.24
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Number of compound SSRs
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Counts
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1,462
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Number of imperfect SSRs
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Counts
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170,017
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Total length of imperfect SSRs
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Bp
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4,825,112
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Table 2. Distribution of mono- to hexa- type of perfect SSRs.
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SSR Type
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No. of SSRs
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Length (bp)
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Percent (%)
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Average
length (bp)
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Relative
abundance (loci/Mb)
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Relative density (bp/Mb)
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Mono
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5,554
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87,503
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14.69
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15.75
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48.81
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769.02
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Di
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17,301
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286,566
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45.75
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16.56
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152.05
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2518.48
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Tri
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12,534
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221,274
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33.15
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17.65
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110.15
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1944.66
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Tetra
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1,781
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38,176
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4.71
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21.44
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15.65
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335.51
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Penta
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425
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11,160
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1.12
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26.26
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3.74
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98.08
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Hexa
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219
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7,146
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0.58
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32.63
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1.92
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62.8
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Table 3. Distribution of di- to hexa- type of perfect SSRs with
three pair of primer.
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SSR Type
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No. of SSRs
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Length (bp)
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Percent (%)
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Average
length (bp)
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Relative
abundance (loci/Mb)
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Relative density (bp/Mb)
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Mono
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2,547
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36,108
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11.26
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14.18
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22.39
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317.35
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Di
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9,149
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144,542
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40.45
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15.80
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80.41
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1270.36
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Tri
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9,351
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160,002
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41.34
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17.11
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82.18
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1406.24
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Tetra
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1168
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24,684
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5.16
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21.13
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10.27
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216.94
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Penta
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277
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7,255
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1.22
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26.19
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2.43
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63.76
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Hexa
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128
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4,194
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0.57
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32.77
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1.12
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36.86
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Figure 1. Distribution of most abundant type of motif
categories.
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Figure 2. SSR repeats distribution of each mono to hexa SSR
types.
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Figure 3. Distribution of different transcription factor
categories predicted in A. paniculata trancriptome.
Table 4. Gene families related to biochemical compound
biosynthesis present in A. paniculata.
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S. No.
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Family Name
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No. of Transcripts
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Function |
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1.
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Cytochrome P450
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359
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Biosynthesis of secondary metabolites |
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2.
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Protein Kinases
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2,762
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Signal transduction pathways |
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3.
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Heat Shock Proteins (HSPs)
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70
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Therapeutic treatments |
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4.
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Transporters
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1,593
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Transport of metabolites |
Figure 4. Distribution of functionally annotated transcripts
of A. paniculata in three main categories of GO classification
viz. Biological Process, Molecular Function, and Cellular Component.
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| Copyright ©
Reg. No. SW-15900/2022 |
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ICAR- National Bureau of Plant Genetic Resources, New Delhi, India |
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| This work is supported by
Indian Council for Agricultural Research, Government of India, New Delhi |
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