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R. Zhou, N. Moshgabadi, K. Adams (2011)
Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploidsProceedings of the National Academy of Sciences, 108
Anna Zdepski, Wenqin Wang, Henry Priest, Faraz Ali, Maqsudul Alam, T. Mockler, T. Michael (2008)
Conserved Daily Transcriptional Programs in Carica papayaTropical Plant Biology, 1
Zhou Du, Xin Zhou, Yi Ling, Zhenhai Zhang, Zhen Su (2010)
agriGO: a GO analysis toolkit for the agricultural communityNucleic Acids Research, 38
A. Paterson, J. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, Alexander Poliakov, J. Schmutz, M. Spannagl, Haibao Tang, Xiyin Wang, T. Wicker, A. Bharti, J. Chapman, F. Feltus, U. Gowik, I. Grigoriev, E. Lyons, C. Maher, Mihaela Martis, A. Narechania, Robert Otillar, Bryan Penning, A. Salamov, Yu Wang, Lifang Zhang, N. Carpita, M. Freeling, A. Gingle, C. Hash, B. Keller, P. Klein, S. Kresovich, M. McCann, R. Ming, D. Peterson, Mehboob-ur-Rahman, D. Ware, P. Westhoff, K. Mayer, J. Messing, D. Rokhsar (2009)
The Sorghum bicolor genome and the diversification of grassesNature, 457
Yu Zhao, Yongfeng Hu, Mingqiu Dai, Limin Huang, Daoxiu Zhou (2009)
The WUSCHEL-Related Homeobox Gene WOX11 Is Required to Activate Shoot-Borne Crown Root Development in Rice[C][W]The Plant Cell Online, 21
Y. Ouyang, Jiongjiong Chen, Weibo Xie, Lei Wang, Qifa Zhang (2009)
Comprehensive sequence and expression profile analysis of Hsp20 gene family in ricePlant Molecular Biology, 70
M. Tamaoki, H. Tsugawa, E. Minami, T. Kayano, N. Yamamoto, Y. Kano-Murakami, M. Matsuoka (1995)
Alternative RNA products from a rice homeobox gene.The Plant journal : for cell and molecular biology, 7 6
Miguel González-Guzmán, G. Pizzio, Regina Antoni, Francisco Vera-Sirera, E. Merilo, G. Bassel, Maria Fernández, M. Holdsworth, M. Perez-Amador, H. Kollist, P. Rodriguez (2012)
Arabidopsis PYR/PYL/RCAR Receptors Play a Major Role in Quantitative Regulation of Stomatal Aperture and Transcriptional Response to Abscisic Acid[C][W]Plant Cell, 24
A. Severin, J. Woody, Yung-Tsi Bolon, Bindu Joseph, B. Diers, A. Farmer, G. Muehlbauer, Rex Nelson, D. Grant, J. Specht, M. Graham, S. Cannon, G. May, C. Vance, R. Shoemaker (2010)
RNA-Seq Atlas of Glycine max: A guide to the soybean transcriptomeBMC Plant Biology, 10
M. Mizutani, D. Ohta (2010)
Diversification of P450 genes during land plant evolution.Annual review of plant biology, 61
Rosario Alonso, L. Oñate-Sánchez, Fridtjof Weltmeier, A. Ehlert, I. Díaz, Katrin Dietrich, J. Vicente-Carbajosa, W. Dröge-Laser (2009)
A Pivotal Role of the Basic Leucine Zipper Transcription Factor bZIP53 in the Regulation of Arabidopsis Seed Maturation Gene Expression Based on Heterodimerization and Protein Complex Formation[W]The Plant Cell Online, 21
G. Son, J. Wan, Hyenchol Kim, X. Nguyen, W. Chung, Jong-Chan Hong, G. Stacey (2012)
Ethylene-responsive element-binding factor 5, ERF5, is involved in chitin-induced innate immunity response.Molecular plant-microbe interactions : MPMI, 25 1
A. Paterson, J. Bowers, B. Chapman (2004)
Ancient polyploidization predating divergence of the cereals, and its consequences for comparative genomics.Proceedings of the National Academy of Sciences of the United States of America, 101 26
T. Hattori, Masako Totsuka, Tokunori Hobo, Y. Kagaya, A. Yamamoto-Toyoda (2002)
Experimentally determined sequence requirement of ACGT-containing abscisic acid response element.Plant & cell physiology, 43 1
G. Feng, Zhixiang Qin, Jin Yan, Xiaoran Zhang, Yuxin Hu (2011)
Arabidopsis ORGAN SIZE RELATED1 regulates organ growth and final organ size in orchestration with ARGOS and ARL.The New phytologist, 191 3
Shipeng Li, G. Os, Shichao Ren, Dali Yu, T. Ketelaar, A. Emons, Chun-Ming Liu (2010)
Expression and Functional Analyses of EXO70 Genes in Arabidopsis Implicate Their Roles in Regulating Cell Type-Specific Exocytosis1[W][OA]Plant Physiology, 154
Guojie Zhang, Guangwu Guo, Xueda Hu, Yong Zhang, Qiye Li, Ruiqiang Li, Ruhong Zhuang, Zhike Lu, Zengquan He, X. Fang, Li Chen, W. Tian, Y. Tao, K. Kristiansen, Xiuqing Zhang, Songgang Li, Huanming Yang, J. Wang, Jun Wang (2010)
Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome.Genome research, 20 5
S. Berri, P. Abbruscato, O. Faivre-Rampant, A. Brasileiro, I. Fumasoni, Kouji Satoh, S. Kikuchi, L. Mizzi, P. Morandini, M. Pè, P. Piffanelli (2009)
Characterization of WRKY co-regulatory networks in rice and ArabidopsisBMC Plant Biology, 9
Mukesh Jain, J. Khurana (2009)
Transcript profiling reveals diverse roles of auxin‐responsive genes during reproductive development and abiotic stress in riceThe FEBS Journal, 276
Jigang Li, Xiaojuan Li, Lei Guo, Feng Lu, Xiaojie Feng, Kun He, Liping Wei, Zhang-liang Chen, Li-jia Qu, H. Gu (2006)
A subgroup of MYB transcription factor genes undergoes highly conserved alternative splicing in Arabidopsis and rice.Journal of experimental botany, 57 6
C. Buchanan, Sanghyun Lim, R. Salzman, Ioannis Kagiampakis, D. Morishige, B. Weers, R. Klein, L. Pratt, M. Cordonnier-Pratt, P. Klein, J. Mullet (2005)
Sorghum bicolor’s Transcriptome Response to Dehydration, High Salinity and ABAPlant Molecular Biology, 58
Martin Calvino, J. Messing (2012)
Sweet sorghum as a model system for bioenergy crops.Current opinion in biotechnology, 23 3
Kenji Yamada, I. Hara-Nishimura, M. Nishimura (2011)
Unique defense strategy by the endoplasmic reticulum body in plants.Plant & cell physiology, 52 12
Miwa Nagae, Masaru Nakata, Yohsuke Takahashi (2008)
Identification of Negative cis-Acting Elements in Response to Copper in the Chloroplastic Iron Superoxide Dismutase Gene of the Moss Barbula unguiculata1Plant Physiology, 146
J. Ehlting, V. Sauveplane, A. Olry, J. Ginglinger, N. Provart, D. Werck-Reichhart (2008)
An extensive (co-)expression analysis tool for the cytochrome P450 superfamily in Arabidopsis thalianaBMC Plant Biology, 8
J Exp Bot
Xiaoyun Dong, Z. Hong, Muthuswamy Sivaramakrishnan, M. Mahfouz, D. Verma (2005)
Callose synthase (CalS5) is required for exine formation during microgametogenesis and for pollen viability in Arabidopsis.The Plant journal : for cell and molecular biology, 42 3
Yao-Ming Chang, Wen-yu Liu, A. Shih, Meng-Ni Shen, Chen-Hua Lu, M. Lu, Hui‐Wen Yang, Tzi-Yuan Wang, Sean Chen, Stella Chen, Wen-Hsiung Li, M. Ku (2012)
Characterizing Regulatory and Functional Differentiation between Maize Mesophyll and Bundle Sheath Cells by Transcriptomic Analysis1[W][OA]Plant Physiology, 160
M. Quint, L. Barkawi, Kai-Ting Fan, J. Cohen, W. Gray (2009)
Arabidopsis IAR4 Modulates Auxin Response by Regulating Auxin Homeostasis1[OA]Plant Physiology, 150
G. Wei, Yi-Wun Pan, J. Lei, Yuxian Zhu (2005)
Molecular cloning, phylogenetic analysis, expressional profiling and in vitro studies of TINY2 from Arabidopsis thaliana.Journal of biochemistry and molecular biology, 38 4
Changqing Zhang, R. Barthelson, G. Lambert, D. Galbraith (2008)
Global Characterization of Cell-Specific Gene Expression through Fluorescence-Activated Sorting of Nuclei1[W][OA]Plant Physiology, 147
N. Fusada, T. Masuda, H. Kuroda, H. Shimada, H. Ohta, K. Takamiya (2005)
Identification of a Novel Cis-Element Exhibiting Cytokinin-Dependent Protein Binding in Vitro in the 5′-region of NADPH-Protochlorophyllide Oxidoreductase Gene in CucumberPlant Molecular Biology, 59
Nadja Baranowskij, Claus Frohberg, Salomé Prat, Lothar Willmitzer (1994)
A novel DNA binding protein with homology to Myb oncoproteins containing only one repeat can function as a transcriptional activator.The EMBO Journal, 13
Chin-Ying Yang, F. Hsu, Jin-Ping Li, N. Wang, M. Shih (2011)
The AP2/ERF Transcription Factor AtERF73/HRE1 Modulates Ethylene Responses during Hypoxia in Arabidopsis1[W][OA]Plant Physiology, 156
Pavana Hiremath, A. Farmer, S. Cannon, Jimmy Woodward, H. Kudapa, Reetu Tuteja, Ashish Kumar, A. Bhanuprakash, Benjamin Mulaosmanovic, Neha Gujaria, L. Krishnamurthy, P. Gaur, P. Kavikishor, T. Shah, R. Srinivasan, M. Lohse, Yongli Xiao, C. Town, D. Cook, G. May, R. Varshney (2011)
Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and AfricaPlant Biotechnology Journal, 9
B. Reddy, S. Ramesh, A. Kumar, S. Wani, R. Ortiz, H. Ceballos, T. Sreedevi (2008)
Bio-Fuel Crops Research for Energy Security and Rural Development in Developing CountriesBioEnergy Research, 1
K. Higo, Y. Ugawa, M. Iwamoto, Tomoko Korenaga (1999)
Plant cis-acting regulatory DNA elements (PLACE) database: 1999Nucleic acids research, 27 1
Yi Jiang, B. Zeng, Hainan Zhao, Mei Zhang, Shaojun Xie, Jinsheng Lai (2012)
Genome-wide transcription factor gene prediction and their expressional tissue-specificities in maize.Journal of integrative plant biology, 54 9
M. Yamaguchi, Nobutaka Mitsuda, M. Ohtani, M. Ohme-Takagi, K. Kato, T. Demura (2011)
VASCULAR-RELATED NAC-DOMAIN7 directly regulates the expression of a broad range of genes for xylem vessel formation.The Plant journal : for cell and molecular biology, 66 4
Dörte Müller, G. Schmitz, K. Theres (2006)
Blind Homologous R2R3 Myb Genes Control the Pattern of Lateral Meristem Initiation in Arabidopsis[W]The Plant Cell Online, 18
N. Syed, M. Kalyna, Yamile Marquez, A. Barta, John Brown (2012)
Alternative splicing in plants – coming of ageTrends in Plant Science, 17
Ehsan Nejad, H. Askari, Sattar Soltani (2012)
Regulatory TGACG-motif may elicit the secondary metabolite production through inhibition of active Cyclin-dependent kinase/Cyclin complexPlant Omics, 5
C. Xie, X. Mao, Jiaju Huang, Yang Ding, Jianmin Wu, Shan Dong, Lei Kong, Ge Gao, Chuan-Yun Li, Liping Wei (2011)
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseasesNucleic Acids Research, 39
S. Filichkin, Henry Priest, S. Givan, Rongkun Shen, Doug Bryant, Samuel Fox, Weng-Keen Wong, T. Mockler (2010)
Genome-wide mapping of alternative splicing in Arabidopsis thaliana.Genome research, 20 1
Dong-Keun Lee, Matt Geisler, P. Springer (2009)
LATERAL ORGAN FUSION1 and LATERAL ORGAN FUSION2 function in lateral organ separation and axillary meristem formation in Arabidopsis, 136
Chung-An Lu, T. Ho, S. Ho, Su-May Yu (2002)
Three Novel MYB Proteins with One DNA Binding Repeat Mediate Sugar and Hormone Regulation of α-Amylase Gene Expression Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.001735.The Plant Cell Online, 14
F. Pinot, F. Beisson (2011)
Cytochrome P450 metabolizing fatty acids in plants: characterization and physiological rolesThe FEBS Journal, 278
Tingting Lu, Guojun Lu, Danlin Fan, Chuanrang Zhu, Wei Li, Qiang Zhao, Qi Feng, Yan Zhao, Yunli Guo, Wenjun Li, Xuehui Huang, B. Han (2010)
Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq.Genome research, 20 9
N. Ishihama, H. Yoshioka (2012)
Post-translational regulation of WRKY transcription factors in plant immunity.Current opinion in plant biology, 15 4
Lan Guo, Junli Zhou, A. Elling, Jean-Benoît Charron, X. Deng (2008)
Histone Modifications and Expression of Light-Regulated Genes in Arabidopsis Are Cooperatively Influenced by Changing Light Conditions1[W][OA]Plant Physiology, 147
Kang-Chang Kim, Zhibing Lai, B. Fan, Zhixiang Chen (2008)
Arabidopsis WRKY38 and WRKY62 Transcription Factors Interact with Histone Deacetylase 19 in Basal Defense[W]The Plant Cell Online, 20
Yukihiro Ito, H. Hirochika, N. Kurata (2002)
Organ-specific alternative transcripts of KNOX family class 2 homeobox genes of rice.Gene, 288 1-2
Diana Dugas, Marcela Monaco, Andrew Olsen, R. Klein, Sunita Kumari, D. Ware, P. Klein (2011)
Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acidBMC Genomics, 12
Braden Walters, Gengkon Lum, G. Sablok, X. Min (2013)
Genome-Wide Landscape of Alternative Splicing Events in Brachypodium distachyonDNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes, 20
C. Moffat, R. Ingle, D. Wathugala, N. Saunders, Heather Knight, M. Knight (2012)
ERF5 and ERF6 Play Redundant Roles as Positive Regulators of JA/Et-Mediated Defense against Botrytis cinerea in ArabidopsisPLoS ONE, 7
Kazuhisa Hiraoka, A. Yamaguchi, Mitsutomo Abe, T. Araki (2013)
The florigen genes FT and TSF modulate lateral shoot outgrowth in Arabidopsis thaliana.Plant & cell physiology, 54 3
D. Burgess (2012)
Alternative splicing: Proteomic rewiring through transcriptomic diversityNature Reviews Genetics, 13
H. Holtan, Simona Bandong, Colleen Marion, L. Adam, Shiv Tiwari, Yu Shen, J. Maloof, D. Maszle, Masa-aki Ohto, S. Preuss, Robert Meister, M. Petracek, P. Repetti, T. Reuber, O. Ratcliffe, R. Khanna (2011)
BBX32, an Arabidopsis B-Box Protein, Functions in Light Signaling by Suppressing HY5-Regulated Gene Expression and Interacting with STH2/BBX21[W][OA]Plant Physiology, 156
Andrew Paterson, K. Schertz, Yann-rong Lin, Sin-Chieh Liu, Yueh-Long Chang (1995)
The weediness of wild plants: molecular analysis of genes influencing dispersal and persistence of johnsongrass, Sorghum halepense (L.) Pers.Proceedings of the National Academy of Sciences of the United States of America, 92 13
F Hu, D Wang, X Zhao, T Zhang, H Sun, L Zhu, F Zhang, L Li, Q Li, D Tao, B Fu, Z Li (2011)
Identification of rhizome-specific genes by genome-wide differential expression analysis in Oryza longistaminataBMC Plant Biol, 11
H. Hurst, O. Hagenbüchle, U. Schibler, P. Shaw, D. Cribbs, P. Wellauer (1986)
REGULATION OF ALPHA-AMYLASE GENE EXPRESSION
Chengsong Zhao, U. Avci, E. Grant, C. Haigler, E. Beers (2007)
XND1, a member of the NAC domain family in Arabidopsis thaliana, negatively regulates lignocellulose synthesis and programmed cell death in xylem.The Plant journal : for cell and molecular biology, 53 3
C Trapnell, L Pachter, SL Salzberg (2009)
TopHat: discovering splice junctions with RNA-SeqBioinformatics, 25
Y. Xiang, M. Song, Zhaoyan Wei, Jianhua Tong, Lixia Zhang, Langtao Xiao, Zhengqiang Ma, Yun Wang (2011)
A jacalin-related lectin-like gene in wheat is a component of the plant defence systemJournal of Experimental Botany, 62
B. Poel, I. Bulens, Yasmin Oppermann, M. Hertog, B. Nicolai, M. Sauter, A. Geeraerd (2013)
S-adenosyl-L-methionine usage during climacteric ripening of tomato in relation to ethylene and polyamine biosynthesis and transmethylation capacity.Physiologia plantarum, 148 2
M. Mikkelsen, M. Thomashow (2009)
A role for circadian evening elements in cold-regulated gene expression in Arabidopsis.The Plant journal : for cell and molecular biology, 60 2
(2014)
Plant Mol Biol
K. Ng, Hao Yu, Toshiro Ito (2009)
AGAMOUS Controls GIANT KILLER, a Multifunctional Chromatin Modifier in Reproductive Organ Patterning and DifferentiationPLoS Biology, 7
A. Mortazavi, B. Williams, Kenneth McCue, Lorian Schaeffer, B. Wold (2008)
Mapping and quantifying mammalian transcriptomes by RNA-SeqNature Methods, 5
Yuxin Hu, Q. Xie, N. Chua (2003)
The Arabidopsis Auxin-Inducible Gene ARGOS Controls Lateral Organ Size Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.013557.The Plant Cell Online, 15
Jacob Washburn, S. Murray, B. Burson, R. Klein, R. Jessup (2012)
Targeted mapping of quantitative trait locus regions for rhizomatousness in chromosome SBI-01 and analysis of overwintering in a Sorghum bicolor × S. propinquum populationMolecular Breeding, 31
RESEARCH ARTICLE Open Access Identification of rhizome-specific genes by genome-wide differential expression Analysis in
Y Hu, Q Xie, NH Chua (2003)
The Arabidopsis auxin-inducible gene ARGOS controls lateral organ sizePlant Cell, 15
R. Salzman, J. Brady, S. Finlayson, C. Buchanan, E. Summer, F. Sun, P. Klein, R. Klein, L. Pratt, M. Cordonnier-Pratt, J. Mullet (2005)
Transcriptional Profiling of Sorghum Induced by Methyl Jasmonate, Salicylic Acid, and Aminocyclopropane Carboxylic Acid Reveals Cooperative Regulation and Novel Gene Responses1[w]Plant Physiology, 138
Alper Yilmaz, M. Nishiyama, Bernardo Fuentes, G. Souza, D. Janies, J. Gray, E. Grotewold (2008)
GRASSIUS: A Platform for Comparative Regulatory Genomics across the Grasses1[W][OA]Plant Physiology, 149
Sungjin Park, Yinghua Huang, P. Ayoubi (2006)
Identification of expression profiles of sorghum genes in response to greenbug phloem-feeding using cDNA subtraction and microarray analysisPlanta, 223
L. Pratt, Chun Liang, Manish Shah, F. Sun, Haiming Wang, S. Reid, A. Gingle, A. Paterson, R. Wing, R. Dean, R. Klein, H. Nguyen, Hong-mei Ma, Xin Zhao, D. Morishige, J. Mullet, M. Cordonnier-Pratt (2005)
Sorghum Expressed Sequence Tags Identify Signature Genes for Drought, Pathogenesis, and Skotomorphogenesis from a Milestone Set of 16,801 Unique Transcripts1[w]Plant Physiology, 139
Norihito Nakamichi, Takatoshi Kiba, Rossana Henriques, T. Mizuno, N. Chua, H. Sakakibara (2010)
PSEUDO-RESPONSE REGULATORS 9, 7, and 5 Are Transcriptional Repressors in the Arabidopsis Circadian Clock[W][OA]Plant Cell, 22
C. Majer, F. Hochholdinger (2011)
Defining the boundaries: structure and function of LOB domain proteins.Trends in plant science, 16 1
Kyu-Ock Yim, D. Bayer (1997)
Rhizome expression in a selected cross in the Sorghum genusEuphytica, 94
Cheol Jang, T. Kamps, D. Skinner, S. Schulze, W. Vencill, Andrew Paterson (2006)
Functional Classification, Genomic Organization, Putatively cis-Acting Regulatory Elements, and Relationship to Quantitative Trait Loci, of Sorghum Genes with Rhizome-Enriched Expression1[W]Plant Physiology, 142
Shuye Jiang, Zhi-gang Ma, J. Vanitha, S. Ramachandran (2013)
Genetic variation and expression diversity between grain and sweet sorghum linesBMC Genomics, 14
H. Mizuno, H. Kawahigashi, Y. Kawahara, H. Kanamori, Jun Ogata, H. Minami, T. Itoh, T. Matsumoto (2012)
Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-interactionBMC Plant Biology, 12
R. Swarup, B. Péret (2012)
AUX/LAX family of auxin influx carriers—an overviewFrontiers in Plant Science, 3
J. Mullet, R. Klein, P. Klein (2002)
Sorghum bicolor - an important species for comparative grass genomics and a source of beneficial genes for agriculture.Current opinion in plant biology, 5 2
Y. Benjamini, Y. Hochberg (1995)
Controlling the false discovery rate: a practical and powerful approach to multiple testingJournal of the royal statistical society series b-methodological, 57
CA Lu, TH Ho, SL Ho, SM Yu (2002)
Three novel MYB proteins with one DNA binding repeat mediate sugar and hormone regulation of alpha-amylase gene expressionPlant Cell, 14
Akshay Kakumanu, Madana Ambavaram, Curtis Klumas, Arjun Krishnan, Utlwang Batlang, Elijah Myers, R. Grene, A. Pereira (2012)
Effects of Drought on Gene Expression in Maize Reproductive and Leaf Meristem Tissue Revealed by RNA-Seq1[W][OA]Plant Physiology, 160
Ruiqiang Li, Yingrui Li, K. Kristiansen, Jun Wang (2008)
SOAP: short oligonucleotide alignment programBioinformatics, 24 5
Zhenlong Xu, Yan-zhou Zhou, C. Meng, Chengjin Guo, Hai-Jiao Xu, Wenjing Lu, Juntao Gu, K. Xiao (2009)
Characterization of promoter expression patterns of OsNrt2.1, a nitrate transporter gene of rice (Oryza sativa L.)Frontiers of Agriculture in China, 3
Karen Loizeau, B. Gambonnet, Guo-Fang Zhang, G. Curien, Samuel Jabrin, D. Straeten, W. Lambert, F. Rébeillé, S. Ravanel (2007)
Regulation of One-Carbon Metabolism in Arabidopsis: The N-Terminal Regulatory Domain of Cystathionine γ-Synthase Is Cleaved in Response to Folate Starvation1[W]Plant Physiology, 145
Leena Salmela, Eric Rivals (2020)
Sequence AnalysisDefinitions
E. Chapman, M. Estelle (2009)
Mechanism of auxin-regulated gene expression in plants.Annual review of genetics, 43
Transcriptomic data for Sorghum propinquum, the wild-type sorghum, are limited in public databases. S. propinquum has a subterranean rhizome and transcriptome data will help in understanding the molecular mechanisms underlying rhizome formation. We sequenced the transcriptome of S. propinquum aerial-shoot and rhizome using an Illumina platform. More than 70 % of the genes in the S. propinquum genome were expressed in aerial-shoot and rhizome. The expression patterns of 1963 and 599 genes, including transcription factors, were specific or enriched in aerial-shoot and rhizome respectively, indicating their possible roles in physiological processes in these tissues. Comparative analysis revealed several cis-elements, ACGT box, GCCAC, GATC and TGACG box, which showed significantly higher abundance in aerial-shoot-specific genes. In rhizome-specific genes MYB and ROOTMOTIFTAPOX1 motifs, and 10 promoter and cytokinin-responsive elements were highly enriched. Of the S. propinquum genes, 27.9 % were identified as alternatively spliced and about 60 % of the alternative splicing (AS) events were tissue-specific, suggesting that AS played a crucial role in determining tissue-specific cellular function. The transcriptome data, especially the co-localized rhizome-enriched expressed transcripts that mapped to the publicly available rhizome-related quantitative trait loci, will contribute to gene discovery in S. propinquum and to functional studies of the sorghum genome. Deep transcriptome sequencing revealed a clear difference in the expression patterns of genes between aerial-shoot and rhizome in S. propinquum. This data set provides essential information for future studies into the molecular genetic mechanisms involved in rhizome formation.
Plant Molecular Biology – Springer Journals
Published: Oct 9, 2013
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