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| Status |
Public on Jan 19, 2016 |
| Title |
RNA-Seq analysis, transcriptome assembly and gene expression profile analysis for Zea may ssp. mexicana L. under cold and drought stress |
| Organism |
Zea mays subsp. mexicana |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: The goals of this study are studies the response of annual Zea mays ssp. mexicana L. under cold and drought stress
Methods: The seedlings of zea may ssp. mexicana L. were generated by Illumina HiSeq2500 deep-sequencing. In order to generate a global overview of Zea mexicana transcriptome data, 3 of complement DNA (cDNA) libraries were prepared from RNA isolated from root, stem, and leave mixed tissues of Zea Mexicana from Control (24℃), Cold (4℃) and Drought (PEG2000, 20%) treatments and each teatment has two repetitions. The sequence reads that passed quality filters were merged and de novo to generate all transcripts set by Trinity with default parameter, which will be treated as reference genome. The number of paired-reads of each sample were mapped to reference genome by Bowtie software v1.1.1 and the number of mapped reads were calculated by RSEM. qRT-PCR validation was performed using BIO-RAD CFX96 sequence detection system and SYBR Green assays.
Results: Using RNA-Seq technology with the Trinity assembled method, we generated a seedling plant transcriptome at a sequencing size of 51.78Gb of Zea mays ssp. mexicana L. from pooled RNA samples which included control (CK), cold (4℃) and drought (PEG2000, 20%) stressed plant samples. A total of 414,232,462 high quality clean reads were used to conduct de novo assembly and annotation of genes without reference genome information. All of these reads were assembled into 251,145 transcripts (N50 = 1,269 bp) and 184,280 unigenes (N50 = 923 bp). A total of 3,504 up-regulated and 1,220 down-regulated genes were detected under cold stress and 532 up-regulated and 82 down-regulated genes were detected under drought stress. A Venn diagram indicated that 208 genes were affected by both cold and drought stresses. 3 cold stress pathways and 5 drought related pathways showed significant KEGG pathways. Functional enrichment analyses identified many common or specific biological processes and gene sets in response to drought and cold stresses. The ABA dependent pathway, trehalose synthetic pathway and CBF6 gene of ICE1-CBF pathway may play important roles in the DEGs co-up-regulated by both stresses of Zea mays ssp. mexicana L.
Conclusions: We analyzed transcriptome data and gene expression profile information from seedlings of Zea mays ssp. mexicana L. under cold and drought stresses. Together these data provides the most comprehensive sequence study available for Zea mays ssp. mexicana L. and provides some important functional genes and molecular mechanism information for improving the quality characteristic of maize in the future.
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| Overall design |
Zea may ssp. mexicana L. "8493" variety mRNA profiles of 13-day seedlings were generated by deep sequencing, in triplicate and 2 repetition using Illumina HiSeq2500 deep-sequencing platform.
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| Contributor(s) |
Lu X, Zhou X, Cao Y, Zhou M, McNeil D, Yang C |
| Citation(s) |
28223998 |
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| Submission date |
Jan 18, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Xiang LU |
| E-mail(s) |
xiang.lu@utas.edu.au
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| Organization name |
University of Tasmania
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| Department |
Tasmania of Institute Agriculture
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| Street address |
Private Bag 98
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| City |
Hobart |
| State/province |
TAS |
| ZIP/Postal code |
7001 |
| Country |
Australia |
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| Platforms (1) |
| GPL21342 |
Illumina HiSeq 2500 (Zea mays subsp. mexicana) |
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| Samples (6)
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| Relations |
| BioProject |
PRJNA309111 |
| SRA |
SRP068562 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76939_Trinity2_cd-hit.fasta.gz |
61.4 Mb |
(ftp)(http) |
FASTA |
| GSE76939_gene_expression_fpkm.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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