RNA-Seq Atlas of Glycine max: A guide to the Soybean Transcriptome

Transcription

1 RNA-Seq Atlas of Glycine max: A guide to the Soybean Transcriptome

2 How do novel structures or functions evolve?

3 A more relevant example Symbiosis and Nitrogen Fixation Limpens & Bisseling (23) Curr. Opin. Plant Biol. 6: 343

4 Genome duplication followed by asymmetric divergence Evlampiev and Isambert BMC Systems Biology 27 1:49 doi:1.1186/

5 Genome duplication in legumes polyploid duplications Innes, R., et al. 28. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiology. How do we examine divergence following duplication? Expression of genes from a common ancestor Epigenetics (e.g. methylation) Genetic variants

6 Soybean Illumina Data Overview Gary Stacey Sample Reads Reads Aligned Reads Uniquely Aligned Apical Meristem 6,477,456 5,669,285 (88%) 3,885,54 (6%) Flower 5,176,14 4,275,733 (83%) 3,322,166 (64%) Green Pods 4,183,24 3,694,647 (88%) 1,442,311 (34%) Leaves 5,29,196 4,74,41 (9%) 2,772,753 (52%) Nodule 6,335,851 5,265,596 (83%) 3,386,46 (53%) Root 6,17,312 5,154,176 (84%) 3,74,765 (61%) Root tip 5,154,499 4,212,283 (82%) 3,187,659 (62%) Read length: 36 Average read quality: Number of gene matches: 43,455-49,992 in JGI 8X Genome

7 Figure 3. Color code maps of gene expression across the the 2 soybean chromosomes. For each chromosome, gene expression (i.e. number of sequence reads/million reads aligned; <.5: yellow,.5-2: orange, 2-5: light green, 5-1: green, 1-25: greenish brown, 25-5: brown, 5-1: brownish red, 1: red) is indicated for nine different tissues (from top to bottom: 84 HAS root hairs, 12 HAS root hairs, nodule, root, root tip, SAM, leaf, flower, pod). The final color strip at the bottom of each chromosome represents gene density (i.e. number of genes per 1Kbp; 1-3 > light grey-black). These maps were generated by using the Comparative map and trait viewer (CMTV) software.

8 Homoeologous Soybean BACs gmw1-15k6 FROM: J. A. Schlueter, J. Y. Lin, S. D. Schlueter et al., BMC Genomics 8 (1), 33 (27). gmw1-15h Soybean lines Soybean li nes 3 Soybean li nes Soybean l ines Soybean lines Soybean lines Soybean li nes Soybean l ines Soybean l ines Soybean l ines Soybean l ines Soybean l i nes Soybean li nes Soybean lines Soybean li nes 2 1 Soybean lines Soybean lines Soybean lines Soybean l ines

9 Duplicated regions in the soybean genome

10 Inter-Homoeolog Differential Expression Tissue p=.5 p=1e-1 Root 7,34 2,168 Root Tip 6,57 1,729 Nodule 6,675 2,31 Apical Meristem 7,462 2,175 Leaves 6,6 1,741 Flower 7,245 2,266 Green Pods 5, Of approximately 14, homoeolog pairs

11 Methylome sequencing in soybean

12 Genome duplication in legumes polyploid duplications Innes, R., et al. 28. Differential accumulation of retroelements and diversification of NB-LRR disease resistance genes in duplicated regions following polyploidy in the ancestor of soybean. Plant Physiology.

13 Synteny Glyma18g499 vs. Medtr7g874 Glyma18g498 Glyma18g499 Glyma18g491 Gm18 Medtr7g872 Mt7 Medtr7g882 Medtr7g874 Gm9 Glyma9g3756 Glyma9g3754

14 Shared duplication expression between Glycine and Medicago 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% % 1% 9% 8% 7% 6% 5% 4% 3% 2% 1% % Nodule Nodule Root Root Leaf Leaf Flower Flower Pod Pod Nodule Nodule Root Root Leaf Leaf Flower Flower Pod Pod Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm Mt Gm

15 Whole Transcriptome Shotgun Sequencing of Soybean High vs Low Protein Lines Four seed developmental timepoints From each of two soybean NILs Each exhibiting either high or low protein content Seed Protein 5 W/W% dry matter 45 4 A B Bolon et. al., 21 BMC Plant Biology Stage

16 Area under the QTL The Seed Protein, Oil, and Yield QTL on Soybean Linkage Group I J. Chunga, H. L. Babkab, G. L. Graefc, P. E. Staswickc, D. J. Leec, P. B. Cregand, R. C. Shoemaker and J. E. Specht: Crop Science 43: (23)

17 Data Summary and Alignment to the Soybean Genome Sample Reads Reads Aligned Reads Uniquely Aligned Total SNPs In/Dels Gm_A1 7,835,63 5,88,687 (74%) 2,99,296 (37%) 1,374,62 4,429 Gm_A2 9,673,118 7,49,621 (77%) 2,662,2 (28%) 1,115,564 6,81 Gm_A3 9,12,649 6,7,125 (74%) 4,788,833 (53%) 1,52,187 4,418 Gm_A4 7,52,993 5,339,938 (76%) 3,519,76 (5%) 915,889 3,457 Gm_B1 16,988,687 13,394,686 (79%) 7,783,311 (46%) 2,61,326 8,545 Gm_B2 7,95,528 6,296,363 (79%) 2,181,665 (27%) 885,383 5,128 Gm_B3 9,21,789 7,4,21 (8%) 4,16,899 (45%) 1,14,933 5,677 Gm_B4 8,99,676 6,831,318 (77%) 4,161,16 (47%) 1,11,387 5,316

18 Supporting gene annotation via RNA-seq in Legumes

19 JGI gene annotated, but all libraries support larger gene model JGI Annotation Region of Read Alignments

20 No gene annotated, but all libraries suggest transcribed region No annotation

21 No gene annotated, expression only in low-protein line A No annotation SNPs Expression only in A

22 Gene expression within QTL region Four differentially expressed genes 124 novel exons Known Genes Novel Exons

23 Decreasing sequence costs over time

24 How can we simultaneously compare (visualize) 1,s of genomes or transcriptomes?

25 Converting nucleotide sequence to ordered pixels

26 Rendering DNA into images A region of human chromosome 17 Conversion of image to grayscale as filter (e.g. methylation) Animation of 1 superimposed images

27 Extensive experience in comparative image analysis software exists in other fields

28 How far can we take this concept? What field has even more experience Maize in visualization? Transcriptomes Breeder Content rated by ESRB