Download

• Additional_files.zip
  • Download all lists, tables, data and figures.

• List_S1.txt
  • List of genes that are transcriptionally active in our study. Two reads mapped to the gene in any of the 14 tissues.
• List_S2.txt
  • List of genes that are transcriptionally active and considered highly confident.
• List_S3.txt
  • List of genes that are transcriptionally active but not considered highly confident.
• List_S4.txt
  • List of genes partitioned by tissue that had a zscore value between 3.4 and 3.6.
• List_S5.csv
  • List of 1000 potential house keeping genes with respective correlation of variance
• List_S6.txt
  • List of genes with a significant increase in gene expression in underground tissues (root and leaf)
• List_S7.txt
  • List of genes with a significant increase in gene expression in seed developmental stages.
• List_S8.txt
  • List of genes witha significant increase in gene expression in aerial tissues(pod, pod-shell, leaf and flower)
• List_S9.txt
  • List of genes with a GOslim annotation of nutrient reservoir activity
• List_S10.txt
  • List of gene with a Goslim annotation of lipoxygenase activity

• Data_S1.pdf
  • Hierarchical clustering dendrogram of genes with a significant increase in gene expression in seed tissues
• Data_S2.pdf
  • Hierarchical clustering dendrogram of genes with a significant increase in gene expression in aerial tissues.
• Data_S3.pdf
  • Hierarchical clustering dendrogram of genes with a significant increase in gene expression in underground tissue.

• 1A_flower.fastq.gz
  • Flower, Soy:001277 (F0.4 Open flower)
• 8A_young_leaf.fastq.gz
  • Young leaf, Soy:000252 (0.4 Leaflets unfurled)
• 5A_-1_seed.fastq.gz
  • Seed, 14-17 DAF, Soy:001290 (S1.06 Cotyledon stage)
• 3A_-2_seed.fastq.gz
  • Seed, 10-13 DAF, Soy:001290 (S1.06 Cotyledon stage)
• 7A_0_seed.fastq.gz
  • Seed, 21 DAF, Soy:001291 (S1.07 Early maturity stage 1)
• 2A_cm_pod.fastq.gz
  • One cm pod, 7 DAF, Soy:001280 (F0.7 Small size pod)
• 6A_-1_shell.fastq.gz
  • Pod-shell, 14-17 DAF, Soy:001282 (F0.9 Full pod size)
• 4A_-2_shell.fastq.gz
  • Pod-shell, 10-13 DAF, Soy:001281 (F0.8 Pod medium size)
• 10A_nodule.fastq.gz
  • Nodule, Soy:001301 (Bacterial root nodule)
• 9A_root.fastq.gz
  • Root, Soy:001183 (Root structures)
• soy_seed_A1.fastq.gz
  • Seed, 25 DAF, Soy:001291 (S1.07 Early maturity stage 1)
• soy_seed_A2.fastq.gz
  • Seed, 28 DAF, Soy:001291 (S1.07 Early maturity stage 1)
• soy_seed_A3.fastq.gz
  • Seed, 35 DAF, Soy:001292 (S1.08 Early maturity stage 2)
• soy_seed_A4.fastq.gz
  • Seed, 42 DAF, Soy:001293 (S1.09 Mid seed maturity)

• Table_S1.xls
  • Summary of short read mapping
• Table_S2.xls
  • Table of genes specific to nodules with high gene expression and corresponding Dana Farber tenative consensus annotation.
• Table_S3.xls
  • Table of genes specific to seed development with high expression and corresponding Dana Farber tenative consensus annotation.
• Table_S4.csv
  • Table of potential housekeeping genes in seed development.
• Table_S5.csv
  • Raw Data: digital gene expression counts of the uniquely mappable reads.
• Table_S6.csv
  • Normalized data: Reads/kilobase/million normalization of the raw data.
• Table_S7.xls
  • Table of genes witha GOslim annotation of nutrient reservior activity found in genes with a preferential gene expression during seed development.

• Figure_1.pdf
  • Hierarchical clustering of tissues based on expression profiles of all genes.
• Figure_2.pdf
  • Z-score analysis of all tissues.
• Figure_3.pdf
  • PDF file version of highest expressed genes without gene names in cells.
• Figure_4.pdf
  • PDF file version of legume specific heatmap without gene names in cells.
• Figure_5.pdf
  • PDF file version of Tissue by Tissue.
• Figure_6.pdf
  • Boxplot-dendrogram of genes with a significant increase in gene expression during seed development.
• Figure_S1.pdf
  • Heatmap of highest expressed genes with gene names in each cell.
• Figure_S2.pdf
  • Heatmap of the legume specific genes with gene names in each cell.

• Script_S1.R
  • This script was used to create the raw data used in this digital gene expression analysis

1. Summary of the RNA-Seq short read sequences
   • This table includes the number of reads that were of low quality, not mappable to the reference genomes, mapped to the B. Rhizobium genome, highly repetitive (mapped to over 100 locations), repetitive (mapped between 2-100 locations), High quality reads (reads that passed our filtering criteria), unique (mapped to 1 location) and total mappable reads (sum of the highly repetitive and high quality reads).
2. Transcriptionally active genes from all predicted gene models
   • List of gene models from all the predicted gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.
3. Transcriptionally active genes from the highly-confident gene models
   • List of gene models from the highly-confident gene models that were transcriptionally active. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model in one or more tissues was greater than 1.
4. Transcriptionally active genes not from the highly-confident gene models
   • List of gene models that were transcriptionally active but not part of the list of genes models that are currently considered highly-confident gene models. A gene model was considered transcriptionally active if the sum of the raw counts that mapped to the model across all tissues was greater than 1.
5. Tissue Specific genes based on Z-score analysis
   • List of gene models that are that have Z-score value between 3.4 and 3.6 in each tissue.
6. Nodule Specific gene expression
   • Genes with high gene expression specific to nodule tissue.
7. Seed specific gene expression
   • Genes with high gene expression specific to seed development.
8. Potential House keeping genes
   • The top 1000 gene models that showed the lowest coefficient of variance (CV) among all the predicted gene models for all 14 tissues (CV = standard deviation/mean).
9. Housekeeping genes in seed development
   • Gene list sorted by coefficient of variance for the seven stages in seed development.
10. Raw short read sequence count data
    • Raw short read sequence count data after our filtering criteria (see methods) but before normalization for every predicted gene model in 14 tissues.
11. RPKM normalized short read sequence count data
    • Short read sequence count data after RPKM normalization for every predicted gene model in 14 tissues.
12. Genes significantly expressed in underground tissues
    • List of gene models for which there was as significant change in gene expression in one of the underground tissues (root and nodule) over all other tissues in this study.
13. Genes significantly expressed in seed tissues
    • List of gene models for which there was as significant change in gene expression in one of the seed tissues (seed 10-DAF, seed 14-DAF, seed 21-DAF, seed 25-DAF, seed 28-DAF, seed 35-DAF and seed 42-DAF) over all other tissues in this study.
14. Genes significantly expressed in aerial tissues
    • List of gene models for which there was as significant change in gene expression in one of the aerial tissues (young leaf, flower, one cm pod, pod-shell 10-DAF, pod-shell 14-DAF) over all other tissues in this study.
15. Hierarchical clustering of genes significantly expressed in seed tissues
    • Hierarchical clustering dendrogram of genes with significant expression in seed tissues.
16. Hierarchical clustering of genes significantly expressed in aerial tissues
    • Hierarchical clustering dendrogram of genes with significant expression in aerial tissues.
17. Hierarchical clustering of genes significantly expressed in underground tissues
    • Hierarchical clustering dendrogram of genes with significant expression in underground tissues.
18. All genes annotated with nutrient reservoir activity
    • List of gene models from all predicted models that have a GOslim annotation of nutrient reservoir activity.
19. Genes annotated with nutrient reservoir activity expressed in seed development
    • Table of gene models with a GOslim annotation of nutrient reservoir activity found in seed development and their possible function based on their homologous Dana Farber tentative consensus sequence.
20. All genes annotated with lipoxygenase activity
    • List of gene models from all predicted models that have a GOslim annotation of lipoxygenase activity.
21. Interval matching script
    • Script to perform interval matching of short read sequence intervals after lignment with GSNAP and predicted gene models (Glyma1.01 genome assembly).
22. Heatmap of highest expressed genes
    • This figure is the actual output from the heatmap.2 R command. Each cell in heatmap for the highest expressed genes contains the name of the gene model.
23. Heatmap of legume specific genes
    • This figure is the actual output from the heatmap.2 R command. Each cell in the heatmap for the legume specific genes contains the name of the gene model.