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tpj12173-sup-0001-FigS1-S16.docxWord document4902K

Figure S1. Fragment distribution of the de novo assembly of ICC4958.

Figure S2. Read depth at assembled bases of chickpea ICC4958 (based on 454/Roche read alignment).

Figure S3. GC content distribution in the genome sequence of chickpea, as compared with other plant species.

Figure S4. Top-20 GO terms represented in the chickpea gene set.

Figure S5. Top-20 PFAM domains represented in the chickpea gene set.

Figure S6. Strategy for the identification of lineage-specific genes in the chickpea genome.

Figure S7. Top-10 GO terms represented in the genes included in chickpea-specific gene families.

Figure S8. Gene distribution in different transcription factor families in chickpea, other sequenced legumes and Arabidopsis.

Figure S9. Phylogenetic analysis of chickpea and Medicago genes belonging to CC-NBS-LRR (a) and Leghaemoglobin (b) families.

Figure S10. Ks distribution analysis of paralogous chickpea gene pairs to determine the genome duplication event.

Figure S11. The whole genome dot plot was generated between chickpea linkage groups (x-axis) and Medicago truncatula chromosome arms (y-axis).

Figure S12. Microsynteny of chickpea (Ca) LG 5 with Medicago truncatula (Mt) chromosome 3.

Figure S13. The whole genome dot plot was generated between chickpea linkage groups (x-axis) and Glycine max chromosome arms (y-axis).

Figure S14. Scatter plot showing the distribution of Ka/Ks (ω) with respect to Ks between gene pairs present in the collinear blocks of chickpea and Medicago.

Figure S15. Ka/Ks distribution analysis of chickpea gene pairs.

Figure S16. Distribution of various GOSlim categories (level 2) in chickpea gene pairs with Ka/Ks > 1.

tpj12173-sup-0002-TableS1-22.docxWord document75K

Table S1. Sequencing data generated for chickpea genotypes.

Table S2. Statistics of draft assembly.

Table S3. Anchoring of scaffolds to linkage groups.

Table S4. Estimation of chickpea genome length based on read alignment.

Table S5. Estimated heterozygosity in ICC4958 draft genome.

Table S6. Transcriptome coverage in the assembled chickpea genome.

Table S7. Repeat content in the assembled chickpea draft genome.

Table S8. Comparative analysis of microsatellite sequences in chickpea draft genome with those in other legumes.

Table S9. Statistics of protein-coding gene prediction.

Table S10. Assessment of gene prediction using the CEGMA pipeline.

Table S11. Experimental evidence for the predicted protein-coding genes.

Table S12. Statistics of protein-coding genes from different plant species.

Table S13. Functional annotation of the predicted protein-coding genes.

Table S14. Features of lineage-specific genes in chickpea.

Table S15. Transcription factor/regulator families in the chickpea draft genome.vTable S16. Comparison of R-gene family in chickpea draft genome with other sequenced plant genomes.

Table S17. Comparison of nodulation-associated gene families in chickpea draft genome with other sequenced plant genomes.

Table S18. Comparison of number of genes associated with carotenoid and flavonoid metabolism in chickpea draft genome with other sequenced plant genomes.

Table S19. Non-coding RNA genes in the chickpea draft genome.

Table S20. Summary of RNA-seq data generated from different tissues/treatments to study gene expression.

Table S21. Summary of tissue-preferential and stress-responsive gene expression results based on RNA-seq data.

Table S22. GO terms enriched in the chickpea genes expressed in tissue-specific manner.

tpj12173-sup-0003-AppendixS1.gzapplication/x-compressed4022KAppendices S1–13. SNP and SSR marker resources.
tpj12173-sup-0004-AppendixS2.xlsapplication/msexcel285K 
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tpj12173-sup-0011-AppendixS9.xlsapplication/msexcel3152K 
tpj12173-sup-0012-AppendixS10.xlsapplication/msexcel3290K 
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tpj12173-sup-0014-AppendixS12.xlsapplication/msexcel3324K 
tpj12173-sup-0015-AppendixS13.xlsapplication/msexcel3489K 
tpj12173-sup-0016-MethodsS1.docxWord document111KMethods S1. Experimental methods and URLs used.
tpj12173-sup-0017-legend.docxWord document124K 

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