Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

The maize leaf transcriptome

ABSTRACT: We have generated over 80 million 32 nt reads generated from RNA samples isolated from the tip and base of a developing Mo17 leaf. A comparision of these data with the maize AGP resulted in the confirmation of approximately 88% of the maize filtered gene set Keywords: Transcriptome analysis Examination of two different RNA samples from two different segments of a developing 3rd leaf

ORGANISM(S): Zea mays

SUBMITTER: Lalit Ponnala

PROVIDER: E-GEOD-16916 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

The B73 maize genome: complexity, diversity, and dynamics.

Schnable Patrick S PS Ware Doreen D Fulton Robert S RS Stein Joshua C JC Wei Fusheng F Pasternak Shiran S Liang Chengzhi C Zhang Jianwei J Fulton Lucinda L Graves Tina A TA Minx Patrick P Reily Amy Denise AD Courtney Laura L Kruchowski Scott S SS Tomlinson Chad C Strong Cindy C Delehaunty Kim K Fronick Catrina C Courtney Bill B Rock Susan M SM Belter Eddie E Du Feiyu F Kim Kyung K Abbott Rachel M RM Cotton Marc M Levy Andy A Marchetto Pamela P Ochoa Kerri K Jackson Stephanie M SM Gillam Barbara B Chen Weizu W Yan Le L Higginbotham Jamey J Cardenas Marco M Waligorski Jason J Applebaum Elizabeth E Phelps Lindsey L Falcone Jason J Kanchi Krishna K Thane Thynn T Scimone Adam A Thane Nay N Henke Jessica J Wang Tom T Ruppert Jessica J Shah Neha N Rotter Kelsi K Hodges Jennifer J Ingenthron Elizabeth E Cordes Matt M Kohlberg Sara S Sgro Jennifer J Delgado Brandon B Mead Kelly K Chinwalla Asif A Leonard Shawn S Crouse Kevin K Collura Kristi K Kudrna Dave D Currie Jennifer J He Ruifeng R Angelova Angelina A Rajasekar Shanmugam S Mueller Teri T Lomeli Rene R Scara Gabriel G Ko Ara A Delaney Krista K Wissotski Marina M Lopez Georgina G Campos David D Braidotti Michele M Ashley Elizabeth E Golser Wolfgang W Kim HyeRan H Lee Seunghee S Lin Jinke J Dujmic Zeljko Z Kim Woojin W Talag Jayson J Zuccolo Andrea A Fan Chuanzhu C Sebastian Aswathy A Kramer Melissa M Spiegel Lori L Nascimento Lidia L Zutavern Theresa T Miller Beth B Ambroise Claude C Muller Stephanie S Spooner Will W Narechania Apurva A Ren Liya L Wei Sharon S Kumari Sunita S Faga Ben B Levy Michael J MJ McMahan Linda L Van Buren Peter P Vaughn Matthew W MW Ying Kai K Yeh Cheng-Ting CT Emrich Scott J SJ Jia Yi Y Kalyanaraman Ananth A Hsia An-Ping AP Barbazuk W Brad WB Baucom Regina S RS Brutnell Thomas P TP Carpita Nicholas C NC Chaparro Cristian C Chia Jer-Ming JM Deragon Jean-Marc JM Estill James C JC Fu Yan Y Jeddeloh Jeffrey A JA Han Yujun Y Lee Hyeran H Li Pinghua P Lisch Damon R DR Liu Sanzhen S Liu Zhijie Z Nagel Dawn Holligan DH McCann Maureen C MC SanMiguel Phillip P Myers Alan M AM Nettleton Dan D Nguyen John J Penning Bryan W BW Ponnala Lalit L Schneider Kevin L KL Schwartz David C DC Sharma Anupma A Soderlund Carol C Springer Nathan M NM Sun Qi Q Wang Hao H Waterman Michael M Westerman Richard R Wolfgruber Thomas K TK Yang Lixing L Yu Yeisoo Y Zhang Lifang L Zhou Shiguo S Zhu Qihui Q Bennetzen Jeffrey L JL Dawe R Kelly RK Jiang Jiming J Jiang Ning N Presting Gernot G GG Wessler Susan R SR Aluru Srinivas S Martienssen Robert A RA Clifton Sandra W SW McCombie W Richard WR Wing Rod A RA Wilson Richard K RK

Science (New York, N.Y.) 20091101 5956

We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of cent ...[more]

PMID: 19965430

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Project description:Plastids contain multiple copies of the plastid chromosome, folded together with proteins and RNA into nucleoids. The degree to which components of the plastid gene expression and protein biogenesis machineries are nucleoid associated, and the factors involved in plastid DNA organization, repair, and replication, are poorly understood. To provide a conceptual framework for nucleoid function, we characterized the proteomes of highly enriched nucleoid fractions of proplastids and mature chloroplasts isolated from the maize (Zea mays) leaf base and tip, respectively, using mass spectrometry. Quantitative comparisons with proteomes of unfractionated proplastids and chloroplasts facilitated the determination of nucleoid-enriched proteins. This nucleoid-enriched proteome included proteins involved in DNA replication, organization, and repair as well as transcription, mRNA processing, splicing, and editing. Many proteins of unknown function, including pentatricopeptide repeat (PPR), tetratricopeptide repeat (TPR), DnaJ, and mitochondrial transcription factor (mTERF) domain proteins, were identified. Strikingly, 70S ribosome and ribosome assembly factors were strongly overrepresented in nucleoid fractions, but protein chaperones were not. Our analysis strongly suggests that mRNA processing, splicing, and editing, as well as ribosome assembly, take place in association with the nucleoid, suggesting that these processes occur cotranscriptionally. The plastid developmental state did not dramatically change the nucleoid-enriched proteome but did quantitatively shift the predominating function from RNA metabolism in undeveloped plastids to translation and homeostasis in chloroplasts. This study extends the known maize plastid proteome by hundreds of proteins, including more than 40 PPR and mTERF domain proteins, and provides a resource for targeted studies on plastid gene expression. Details of protein identification and annotation are provided in the Plant Proteome Database.

Project description:To investigate the developmental gradient of the third maize leaf, the light exposed area of the leaf (corresponding to 18cm of leaf) and 2cm shaded by the sheath were sampled in ten slices. Four replicates were collected, immediately shock frozen in liquid nitrogen and subsequently cut into 2cm slices. At least 10 plants were pooled for each biological replicate. We have systematically analyzed a developmental gradient of the third maize leaf from the point of emergence into the light to the tip in ten continuous leaf slices to study organ development and physiological and biochemical functions. Transcriptome analysis, oxygen sensitivity of photosynthesis, delta-13C values, and photosynthetic rate measurements showed that the maize leaf undergoes a sink to source transition without an intermediate phase of C3 photosynthesis or operation of a photorespiratory carbon pump. Metabolome and transcriptome analysis, chlorophyll and protein measurements, as well as dry weight determination showed continuous gradients for all analyzed items. The absence of binary on-off switches and regulons pointed to a morphogradient along the leaf as the determining factor of developmental stage. Analysis of transcription factors for differential expression along the leaf gradient defined a list of putative regulators orchestrating the sink-to-source transition and establishment of C4 photosynthesis. Finally, transcriptome and metabolome analysis, as well as enzyme activity measurements, and absolute quantification of selected metabolites revised the current model of maize C4 photosynthesis. All datasets are included within the publication to serve as a resource for maize leaf systems biology. For the transcriptional analysis, the goal of the study was to (i) identify whether the leaf contains binary switches for genes involved in photosynthesis, (ii)characterize the patterns of gene expression in the leaf, (iii) provide independent validation of maize leaf expression experiments published in Li et al. (2011) and (iv) determine transcripts co-expressed with key transcripts of C4 photosynthesis. To this end, changed transcripts were determined by ANOVA and characterized by K-means and hierachical clustering. Four replicates were collected for each of the ten consecutive leaf slices resulting in 40 one color arrays. Slice 1 represents the tip of the leaf, slice 10 the lowermost slice which is shaded by the sheath with all slices in between consecutively numbered.

Project description:As maize seedlings germinate into the soil, they encounter an environment teeming with insects seeking rich sources of nutrition. Maize presumably has developed a number of molecular mechanisms to ensure survival at the beginning of its life cycle. Bioassays indicated maize seedlings were more toxic to caterpillars than shoots from 3 or 4 leafed plants. Microarray technology was utilized to document the expression of a number of genes with potential defensive functions in seedling tissue. In addition to elevated levels of the genes involved in the biosynthesis of DIMBOA (2,4-dihydroxy-7-methoxy-1,4-benzoxazin-3-one), an anti-insect resistance molecule, other highly expressed genes in the seedling encode the following putative proteins: defensin, hydroxyproline and proline-rich protein, thaumatin-like protein, lipase, cystatin, protease inhibitor, and a variety of proteases. Changes in the levels of gene expression by the microarray technology were well correlated to results using quantitative RT-PCR. The potential resistance genes identified occurred mainly on chromosomes 1 and 5 in the B73 genome. Analysis of promoters of four DIMBOA biosynthetic genes determined that a Dof transcription factor, two of which were differentially expressed in three vegetative stages, is possibly involved in regulation of the DIMBOA biosynthetic pathway. The results indicate that maize employs a wide variety of potential resistance mechanisms in seedling tissue to resist a possible insect attack. Three different Zea mays plant (B73) life stages were sampled: a) seedlings, which had grown just above the soil line, which also served as reference tissue (reference tissue was always labeled Cy5 and consisted of leaf shoots pooled from 12 plants); b) leaf shoots from plants with four leaves; and c) leaf shoots from plants with six leaves. There were 3 samples (biological replications) of each treatment (6 plants per sample) and the samples were labeled Cy3 and which were combined with a reference chip for a total of 9 chips: (3 biological replicates of seedling, 4 leaf stage and 6 leaf stage).

Dataset Information

The maize leaf transcriptome

Publications

The B73 maize genome: complexity, diversity, and dynamics.

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