Table 1.
Assembly optimization/validation of Illumina and Roche 454 data of kabuli chickpea.
Table 2.
Statistics/validation of hybrid assembly of Ilumina and Roche 454 data of kabuli chickpea.
Figure 1.
GOSlim term assignment to the transcripts of three chickpea types in different categories of biological process, molecular function and cellular component.
Data for desi and wild chickpeas are from our previous studies [5], [6].
Figure 2.
SSR distribution in kabuli, desi and wild chickpea types.
(A) Distribution of total number of SSRs identified in kabuli chickpea in different classes. (B) Distribution of polymorphic SSRs identified in kabuli/desi and kabuli/wild chickpea. (C) Frequency difference of different classes of polymorphic SSRs identified in kabuli/desi and kabuli/wild chickpea.
Figure 3.
Frequency of different polymorphic SSR types.
Number of polymorphic SSRs in kabuli/desi (A) and kabuli/wild (B) chickpea representing different repeat types are shown.
Table 3.
Average repeat length and unit size of different SSR-types in three chickpea genotypes.
Figure 4.
Frequency and substitution types of the identified SNPs.
(A) The total number of transcripts (primary axis) and SNPs (secondary axis) having different SNP frequency is given. (B) The frequency of different substitution types is shown.
Table 4.
SNP frequency among different chickpea genotypes.
Figure 5.
Distribution of SNPs in tissue-specific and transcription factor encoding transcripts.
The number of tissue-specific (A,B) and transcription factor encoding (C,D) transcripts containing at least one SNP and total number of SNPs present in them are represented for kabuli/desi (A,C) and kabuli/wild (B,D).
Figure 6.
Experimental validation of in silico identified polymorphic SSRs and SNPs.
(A) Experimental validation of polymorphic SSRs. Representative gels showing PCR amplification of polymorphic SSRs validating the length polymorphism between three chickpea genotypes, kabuli (1), desi (2) and wild (3) as expected. The PCR amplicons were resolved in 3.5% MetaPhor agarose gel. (B) Large-scale validation and polymorphism potential of selected SSRs in kabuli and desi genotypes. Representative gels showing PCR amplification of selected SSRs validating the length polymorphism in various chickpea genotypes (as indicated on the top of each lane). The PCR amplicons were resolved in 3.5% MetaPhor agarose gel. (C) Experimental validation of polymorphic SNPs by allele-specific PCR genotyping assay. Representative gels showing allele-specific fragment length variations of SNPs validating the polymorphism between kabuli (1) and desi (2) as expected. The PCR amplicons were resolved in 2.5% MetaPhor agarose gel. M, 50 bp DNA ladder as size standard.
Figure 7.
Distribution of synonymous substitution rate (Ks) value and Ka/Ks ratio among the orthologous transcript pairs between different chickpea types.
(A,B) Distribution of Ks value among the orthologous transcript pairs between kabuli and desi (A), and kabuli and wild (B). The secondary peak (marked by arrow) in Ks distribution of orthologs indicates the speciation event. Inset represents enlarged version of the graph showing secondary peak. (C,D) Frequency distribution of Ka/Ks ratio in orthologous pairs between kabuli and desi (C) and kabuli and wild (D). The average value of Ka/Ks ratio is shown by arrow head.