Overview
Analysis Namede novo Green Ash Ozone Treatment Experiment
Transcriptome NameGreen Ash Ozone
MethodTrinity
SourceGreen Ash Ozone
Date performed2012-12-19
Number of Contigs63,113

This project aims to elucidate the molecular response of hardwood tree seedlings to varying levels of ozone concentration. Ozone pollution places environmental stress on forest trees resulting in early leaf senescence and loss of photosynthetic capacity. Such environmental stress poses a major challenge for high productivity and quality. Data from other species:

The experimental design included 4 levels of ozone across 3 exposure lengths. Green ash seedlings were randomly assigned to 12 experimental groups:

  • Seedlings exposed to normal atmosphere for 7 hours (control)
  • Seedlings exposed to 80 ppb of ozone for 7 hours
  • Seedlings exposed to 125 ppb of ozone for 7 hours
  • Seedlings exposed to 225 ppb of ozone for 7 hours
  • Seedlings exposed to normal atmosphere for 14 days (control)
  • Seedlings exposed to 80 ppb of ozone for 14 days
  • Seedlings exposed to 125 ppb of ozone for 14 days
  • Seedlings exposed to 225 ppb of ozone for 14 days
  • Seedlings exposed to normal atmosphere for 28 days (control)
  • Seedlings exposed to 80 ppb of ozone for 28 days
  • Seedlings exposed to 125 ppb of ozone for 28 days
  • Seedlings exposed to 225 ppb of ozone for 28 days

At the end of the exposure time, mRNA was isolated from the leaf tissue of seedlings. The RNA was barcoded, pooled and sequenced using the Illulmina platform, yielding paired end reads of 151 x 151 bases.

Read Statistics

Library Reads Bases
GA1 - 7 hrs, control 419,064 63,278,664
GA2 - 7 hrs, 80ppb 457,118 69,024,818
GA3 - 7 hrs, 125ppb 495,728 74,854,928
GA4 - 7 hrs, 225ppb 500,118 75,517,818
GA5 - 14 days, control 450,932 68,090,732
GA6 - 14 days, 80ppb 427,298 64,521,998
GA7 - 14 days, 125ppb 507,634 76,652,734
GA8 - 14 days, 225ppb 483,742 73,045,042
GA9 - 28 days, control 440,864 66,570,464
GA10 - 28 days, 80ppb 486,950 73,529,450
GA11 - 28 days, 125ppb 516,644 78,013,244
GA12 - 28 days, 250ppb 318,888 48,152,088

Sequenced reads were trimmed with Trimmomatic and assembled with Trinity.

Assembly Statistics

Number of Putative Transcripts 63,113
Number of Components 42,216
Putative Transcript N50 1,184bp
Putative Transcript Average Length 791

Download assembled data:

Putative Transcripts (fasta format)
Predicted ORFs (fasta format)