Summary
Name
Liriodendron tulipifera - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Liriodendron tulipifera
Data Source
Source Name
: de novo assembly
Source Version
: 101314
Date Performed
Sunday, October 12, 2014 - 21:00
Number of transcripts
58249
Average Transcript Length
835
Program, Pipeline, Workflow or Method Name
Trinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST
Program Version
trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27
Cross Reference
Description and Download
Description: 
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.
MiSeq reads from seven libraries were cleaned with Trimmomatic and assembled by Trinity. CD-hit with parameter -c 0.95 was used to collapse highly similar reads into a single sequence. Protein sequences were predicted using Trinity. Data has been uploaded to NCBI ( go to NCBI BioProject page).

Assembly Statistics

Number of Transcripts58,249
Transcript N501,360 bp
Transcript Average Length835 bp
Number of Proteins31,347
Protein N50378 aa
Protein Average Length297 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 47% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 70% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 63% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 89% of proteins matched a Trembl plant entry
InterProScan search
Excel output
SSR Pipeline
Excel file with statistics, SSR motifs and primers (489 predicted high quality markers)

Read Statistics

RNA was sampled from leaves of seedlings exposed to ozone levels (control, 80ppm, 125ppm, or 225ppm) at 7 hours, 14 days, 28 days, and 29 days with mechanical wounding. Raw data has been uploaded to the NCBI Short Read Archive. Links are included below.

Illumina MiSeq Data

Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Tulip Poplar 29Day 80ppb + mechanical woundingTP-29Day-80bIllumina MiSeq308,29583,923,357
Tulip Poplar 7hr ControlTP-7HR-CoIllumina MiSeq1,023,282285,127,021
Tulip Poplar 7hr 80ppbTP-7HR-80ppbIllumina MiSeq1,073,063297,925,470
Tulip Poplar 7hr 225ppbTP-7HR-225ppbIllumina MiSeq2,670682,174
Tulip Poplar 7hr 125ppbTP-7HR-125ppbIllumina MiSeq1,139,738319,099,431
Tulip Poplar 29Day Control + mechanical woundingTP-29Day-COIllumina MiSeq1,226,283342,140,055
Tulip Poplar 29Day 80ppb + mechanical woundingTP-29Day-80Illumina MiSeq1,489,683403,528,313
Tulip Poplar 29Day 225ppb + mechanical woundingTP-29Day-225Illumina MiSeq1,514,523419,972,720
Tulip Poplar 29Day 125ppb + mechanical woundingTP-29Day-125Illumina MiSeq1,241,972345,692,911
Tulip Poplar 28Day ControlTP-28Day-COIllumina MiSeq1,617,874445,921,831
Tulip Poplar 28Day 80ppbTP-28Day-80Illumina MiSeq864,164233,018,505
Tulip Poplar 28Day 225ppbTP-28Day-225Illumina MiSeq1,175,094320,066,671
Tulip Poplar 28Day 125ppbTP-28Day-125Illumina MiSeq1,183,664333,688,621
Tulip Poplar 14Day ControlTP-14DAy-CoIllumina MiSeq785,027213,273,306
Tulip Poplar 14Day 80ppbTP-14DAy-80ppbIllumina MiSeq731,463195,163,223
Tulip Poplar 14Day 225ppbTP-14DAy-225ppbIllumina MiSeq340,81095,943,980
Tulip Poplar 14Day 125ppbTP-14DAy-125ppbIllumina MiSeq682,722187,819,053
TOTAL16,400,3274,522,986,642
In addition to the miSeq reads from the ozone experiments, two other sources of transcripts were used for the assembly. 2.3 million 454 reads from the ancestral genome project and 24,663 reads from the EST division of NCBI.
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