scholarly journals Experimental Design for Laser Microdissection RNA-Seq: Lessons from an Analysis of Maize Leaf Development

10.3791/55004 ◽  
2017 ◽  
Author(s):  
Robyn M. Johnston ◽  
Anne W. Sylvester ◽  
Michael J. Scanlon
Keyword(s):  
Experimental Design ◽  
Leaf Development ◽  
Laser Microdissection ◽  
Rna Seq ◽  
Maize Leaf

scholarly journals Transcriptome Analysis of Ginkgo biloba L. Leaves across Late Developmental Stages Based on RNA-Seq and Co-Expression Network

Forests ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 315
Author(s):  
Hailin Liu ◽  
Xin Han ◽  
Jue Ruan ◽  
Lian Xu ◽  
Bing He
Keyword(s):  
Ginkgo Biloba ◽  
Leaf Development ◽  
Developmental Stages ◽  
Leaf Growth ◽  
Rna Seq ◽  
Final Size ◽  
Dioecious Species ◽  
Related Factors ◽  
New Genes ◽  
Gene Modules

The final size of plant leaves is strictly controlled by environmental and genetic factors, which coordinate cell expansion and cell cycle activity in space and time; however, the regulatory mechanisms of leaf growth are still poorly understood. Ginkgo biloba is a dioecious species native to China with medicinally and phylogenetically important characteristics, and its fan-shaped leaves are unique in gymnosperms, while the mechanism of G. biloba leaf development remains unclear. In this study we studied the transcriptome of G. biloba leaves at three developmental stages using high-throughput RNA-seq technology. Approximately 4167 differentially expressed genes (DEGs) were obtained, and a total of 12,137 genes were structure optimized together with 732 new genes identified. More than 50 growth-related factors and gene modules were identified based on DEG and Weighted Gene Co-expression Network Analysis. These results could remarkably expand the existing transcriptome resources of G. biloba, and provide references for subsequent analysis of ginkgo leaf development.

scholarly journals Parallel Proteomic and Phosphoproteomic Analyses of Successive Stages of Maize Leaf Development

2013 ◽  
Vol 25 (8) ◽  
pp. 2798-2812 ◽  
Author(s):  
Michelle R. Facette ◽  
Zhouxin Shen ◽  
Fjola R. Björnsdóttir ◽  
Steven P. Briggs ◽  
Laurie G. Smith
Keyword(s):  
Leaf Development ◽  
Maize Leaf

scholarly journals Specification of adaxial cell fate during maize leaf development

Development ◽  
2004 ◽  
Vol 131 (18) ◽  
pp. 4533-4544 ◽  
Author(s):  
M. T. Juarez
Keyword(s):  
Cell Fate ◽  
Leaf Development ◽  
Maize Leaf

scholarly journals Maize leaf development under climate change scenarios

2010 ◽  
Vol 45 (11) ◽  
pp. 1227-1236
Author(s):  
Nereu Augusto Streck ◽  
Josana Andréia Langner ◽  
Isabel Lago
Keyword(s):  
Climate Change ◽  
Elevated Temperature ◽  
Air Temperature ◽  
Leaf Development ◽  
Flag Leaf ◽  
Climate Change Scenarios ◽  
Crop Failure ◽  
Maize Leaf ◽  
Late Emergence ◽  
Leaf Appearance

The objective of this work was to simulate maize leaf development in climate change scenarios at Santa Maria, RS, Brazil, considering symmetric and asymmetric increases in air temperature. The model of Wang & Engel for leaf appearance rate (LAR), with genotype-specific coefficients for the maize variety BRS Missões, was used to simulate tip and expanded leaf accumulated number from emergence to flag leaf appearance and expansion, for nine emergence dates from August 15 to April 15. LAR model was run for each emergence date in 100-year climate scenarios: current climate, and +1, +2, +3, +4 and +5°C increase in mean air temperature, with symmetric and asymmetric increase in daily minimum and maximum air temperature. Maize crop failure due to frost decreased in elevated temperature scenarios, in the very early and very late emergence dates, indicating a lengthening in the maize growing season in warmer climates. The leaf development period in maize was shorter in elevated temperature scenarios, with greater shortening in asymmetric temperature increases, indicating that warmer nights accelerate vegetative development in maize.

Genome-wide transcript analysis of early maize leaf development reveals gene cohorts associated with the differentiation of C4Kranz anatomy

2013 ◽  
Vol 75 (4) ◽  
pp. 656-670 ◽  
Author(s):  
Peng Wang ◽  
Steven Kelly ◽  
Jim P. Fouracre ◽  
Jane A. Langdale
Keyword(s):  
Leaf Development ◽  
Transcript Analysis ◽  
Maize Leaf ◽  
Genome Wide

scholarly journals Short paired-end reads trump long single-end reads for expression analysis

2019 ◽  
Author(s):  
Adam H. Freedman ◽  
John M. Gaspar ◽  
Timothy B. Sackton
Keyword(s):  
Experimental Design ◽  
Differential Expression ◽  
Expression Analysis ◽  
Cost Effective ◽  
Rna Seq ◽  
Cost Effective Approach ◽  
Effective Manner ◽  
Gene Level ◽  
Highly Correlated ◽  
Paired End Sequencing

ABSTRACTBackgroundTypical experimental design advice for expression analyses using RNA-seq generally assumes that single-end reads provide robust gene-level expression estimates in a cost-effective manner, and that the additional benefits obtained from paired-end sequencing are not worth the additional cost. However, in many cases (e.g., with Illumina NextSeq and NovaSeq instruments), shorter paired-end reads and longer single-end reads can be generated for the same cost, and it is not obvious which strategy should be preferred. Using publicly available data, we test whether short-paired end reads can achieve more robust expression estimates and differential expression results than single-end reads of approximately the same total number of sequenced bases.ResultsAt both the transcript and gene levels, 2×40 paired-end reads unequivocally provide expression estimates that are more highly correlated with 2×125 than 1×75 reads; in nearly all cases, those correlations are also greater than for 1×125, despite the greater total number of sequenced bases for the latter. Across an array of metrics, differential expression tests based upon 2×40 consistently outperform those using 1×75.ConclusionResearchers seeking a cost-effective approach for gene-level expression analysis should prefer short paired-end reads over a longer single-end strategy. Short paired-end reads will also give reasonably robust expression estimates and differential expression results at the isoform level.

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