Open Access Highly Accessed Research article

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

Diana V Dugas1, Marcela K Monaco2, Andrew Olson2, Robert R Klein3, Sunita Kumari2, Doreen Ware24 and Patricia E Klein1*

Author Affiliations

1 Department of Horticulture, Texas A&M University, College Station, TX 77843, USA

2 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA

3 USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77843, USA

4 USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY 14853, USA

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BMC Genomics 2011, 12:514  doi:10.1186/1471-2164-12-514

Published: 18 October 2011

Additional files

Additional file 1:

Lane by lane summary of RNA-Seq data. Read mapping to splice junctions included within the total number of reads mapped to genes.

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Additional file 2:

Pearson correlation coefficients for roots and shoots across all runs

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Additional file 3:

Differentially expressed genes in treatment vs. control roots and shoots based on a 2X sequencing depth. aConfidences refer to those assigned to the gene models by Patterson et. al [43]. bABI3VP1 - proteins containing a B3 domain and named after the founding members (ABA INSENSITIVE 3 and VIVIPAROUS1); AP2 - Apetela2-like proteins that contain one repeated AP2/ERF domain; AP2-EREBP - Apetela2 and Ethylene-responsive element binding proteins containing two repeated AP2/ERF domains; ARF - auxin response factor family members; ARR-B - members of the type-B phospho-accepting response regulator family; AUX/IAA - auxin/indole-3-acetic acid family members controlled by auxin-responsive elements (AuxREs); B3 - Superfamily that encompasses the auxin response factor family, and the LAV, RAV and REM family containing an ~110 amino acid region called the B3 domain; bHLH - basic helix-loop-helix protein; bZIP - basic leucine zipper protein; C2C2-CO-like - similar to "CO-like"; C2C2-Dof - proteins containing DNA-binding with one finger domain and a highly conserved DNA-binding domain, which includes a single C2-C2 zinc finger; C2C2-GATA - GATA-binding proteins containing one or two highly conserved zinc finger DNA-binding domains; C2C2-YABBY - proteins containing a C2C2 zinc finger-like domain towards the amino terminus and a helix-loop-helix (YABBY) domain; C2H2 - proteins containing zinc finger domains with a secondary structure stabilized by a zinc ion bound to the Cys and His residues of the finger; C3H - proteins containing a Cys3His zinc finger domain; CCAAT - proteins contained within the NF-A complex that recognize CCAAT box motifs; CCAAT-HAP2 - HAP2 proteins of the heterotrimeric CCAAT-box-binding complex (HAP2, HAP3, and HAP5); CO-like - CONSTANS-like proteins, containing both a zinc-finger and CCT (CO, CO-like, TOC1) domain; CPP - cysteine-rich polycomb-like proteins containing one or two Cys-rich domains; DBB - proteins containing double B-box zinc finger domains; Dof - proteins containing DNA-binding with one finger domain; EIL - EIN-3-like transcription factors involved in ethylene signaling; ERF - ethylene-responsive factors; FAR1 - far-red-impaired response family members; G2-like - proteins similar to G2 (maize); GATA - proteins that interact with conserved WGATAR; GeBP - proteins similar to GL1 enhancer binding protein and containing a central region with no known motifs and a C-terminal region with a putative leucine-zipper motif; GNAT - Gcn5-related N-acetyltransferase superfamily members; GRAS - named for GAI, RGA, SCR family members; GRF - proteins containing the same QLQ and WRC domains found in GROWTH-REGULATING FACTOR1 (GRF1); HB - similar to "Homeobox"; HD-ZIP - proteins containing a homeodomain and leucine zipper motif; HMG - proteins containing high-mobility-group boxes initially identified as DNA-binding domains; Homeobox - homeobox proteins; HSF - heat shock factor proteins; Jumonji - proteins that contain JmjN and JmjC domains and may be protein hydroxylases that catalyse a novel histone modification; LBD and LOB-LATERAL ORGAN BOUNDARIES domain containing proteins which bind to GCGGCG; LSD - proteins that contain three zinc finger domains; M-type - similar to "MADS"; MADS - MINICHROMOSOME MAINTENANCE 1 (MCM1) from S. cerevisiae AGAMOUS (AG) from Arabidopsis thaliana, DEFICIENS (DEF) from Antirrhinum majus and SERUM RESPONSE FACTOR (SRF) from Homo sapiens) family members; MBF1 - proteins similar to multiprotein bridging factor 1 and mediators of transcriptional activation by bridging between an activator and a TATA-box binding protein (TBP); MIKC - type-II MADS-box containing proteins; mTERF - proteins containing repetitions of a 30 amino acid module, the mTERF motif, containing leucine zipper-like heptads; MYB - proteins containing the MYB (from the oncogene of avian myeloblastosis virus) domain; MYB-related - proteins containing MYB-related domains; NAC - named for NAM, ATAF, and CUC family members; NF-YA - the A subunit of the NF-Y complex that recognizes CCAAT box motifs; NF-YB - the B subunit of the NF-Y complex that recognizes CCAAT box motifs; Nin-like - nodule inception-like proteins; OFP - ovate family proteins contain a conserved C-terminal domain; Orphans - transcription factors that don't belong to any of the other families -- from GrassTFDB; PHD - proteins containing a Plant Homeo Domain finger that resembles the metal binding RING domain (Cys3-His-Cys4) and FYVE domain; PLATZ - proteins similar to PLATZ1 (plant AT-rich sequence- and zinc-binding protein 1) zinc-dependent DNA-binding protein; Pseudo ARR-B - type-B phospho-accepting response regulator proteins; RAV - proteins containing both a B3 domain and a single AP2/ERF domain; RWP-RK - proteins containing a RWP-RK domain; SBP - proteins encoding a conserved protein domain of 76 amino acids in length (SBP-domain); SET - proteins containing a 130-residue SET domain (named after three Drosophilia genes involved in epigenetic processes, Su(var), E(z) and trithorax); Sigma70-like - proteins similar to sigma70; SNF2 - proteins with seven characteristic blocks comprising the helicase region; TALE - three-amino-acid-loop-extension class of homeoproteins contains the KNOTTED-like homeodomain (KNOX) and BEL1-like Homeodomain (BELL) members; TAZ - proteins containing a TAZ2 zinc finger; TCP - proteins containing the TCP (from teosinte branched1from maize, CYCLOIDEA from snapdragon, and the PROLIFERATING CELL FACTORS 1 and 2 from rice) domain, a 59-amino acid basic helix-loop-helix motif; Tify - proteins containing a TIFY domain (named for the most conserved amino acids); Trihelix - proteins containing helix-loop-helix-loop-helix domains; TUB - proteins containing C-terminal tubby domains; Uncategorized - transcription factors that don't belong to any of the other families -- GrassTFDB and PlnTFDB; WOX - homeobox proteins containing a conserved DNA-binding homeodomain; WRKY - proteins containing the WRKYGQK sequence followed by a C2H2 or C2HC zinc finger motif; YABBY - similar to "C2C2-YABBY"; ZF-HD - zinc finger homeodomain proteins

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Additional file 4:

All genes differentially expressed under ABA- or PEG-treatment

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Additional file 5:

Oligonucleotides used for qRT-PCR. aGeneIDs in bold have unknown protein function. bqPCR results comparing treated vs. control samples; passed - qPCR results agreed with RNA-Seq data; failed - qPCR results did not agree with RNA-Seq data.

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Additional file 6:

Enrichment p-values for GO biological processes categories. aGO categories falling under Other do so because they are found as enriched for groups of DE genes which are not easily grouped according to differential expression in tissue or treatment.

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Additional file 7:

SorghumCyc pathway Z-score enrichment analysis for genes differentially expressed in treatment vs. control roots and shoots. ¹Observed Counts = The number of DE genes found within a given pathway. 2Expected Counts = The number of DE genes expected within a given pathway based on the size of the pathway and DE gene list (see Methods). 3A Z-score ≥ 2 with a corresponding p-value ≤ 0.05 is indicative of an enriched pathway.

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Additional file 8:

Ratio of reactions containing differentially expressed genes to the total number of reactions within annotated pathways. aPathways are only included in this list if they contain 3 or more reactions.

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Additional file 9:

p-Values for cis-element enrichment within 1000 bp from the transcription start sites for differentially expressed genes in response to ABA- and PEG-treatment. †B (CGT); D (AGT); H (ACT); K (GT); M (AC); N (ACGT); R (AG); S (CG); V (ACG); W (AT); Y (CT)

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Additional file 10:

Ortholog gene pairs of unknown function important in drought response. a[145]; b[26]; c[13]; d[17]; e[30]

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Additional file 11:

p-Values for cis-element enrichment in 1000 bp upstream of the transcriptional start site for sorghum genes with unknown function conserved in function and expression across species. †B (CGT); D (AGT); H (ACT); K (GT); M (AC); N (ACGT); R (AG); S (CG); V (ACG); W (AT); Y (CT)

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Additional file 12:

p-Values for cis-element enrichment in 1000 bp upstream of the transcriptional start site for rice, maize, and Arabidopsis genes with unknown function conserved in function and expression to sorghum. †B (CGT); D (AGT); H (ACT); K (GT); M (AC); N (ACGT); R (AG); S (CG); V (ACG); W (AT); Y (CT)

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Additional file 13:

Number of genes within read count bins

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