Summary
Name
[Archived] Nyssa sylvatica - Transcriptome Assembly v120313
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Nyssa sylvatica
Data Source
Source Name
: de novo assembly
Source Version
: 120313
Date Performed
Monday, December 2, 2013 - 20:00
Number of transcripts
55630
Average Transcript Length
760
Program, Pipeline, Workflow or Method Name
Trinity; CD-HIT-EST
Program Version
trinityrnaseq_r2013-11-10, cd-hit-v4.6.1-2012-08-27
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 eight 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.

Assembly Statistics

Number of Transcripts55,630
Transcript N501,172 bp
Transcript Average Length760 bp
Number of Proteins30,838
Protein N50338 aa
Protein Average Length275 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 53% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 72% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-5 cutoff - 76% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 96% of proteins matched a Trembl plant entry
HMMER search against Pfam database
Excel output of all hits
Proteins assigned to GO terms inferred from pfam hits
SSR Pipeline
Excel file with statistics, SSR motifs and primers (504 predicted high quality markers)
Fasta file of sequences with an SSR repeat and primers (504 sequences)

Read Statistics

RNA was sampled from leaves of seedlings exposed to ozone levels (control, 80ppm, 125ppm, or 225ppm) for 7 hours and 14 days. Raw data is being uploaded to the NCBI Short Read Archive. Links will be added when they are available.
Library DescriptionMiSeq ReadsMiSeq Bases
14Day 125ppb 962,642 129,723,233
14Day 125ppb 962,642 129,898,426
14Day 225ppb 1,210,565 158,722,565
14Day 225ppb 1,210,565 158,936,867
14Day 80ppb 1,159,659 158,033,236
14Day 80ppb 1,159,659 158,194,028
14Day Control 959,894 133,589,707
14Day Control 959,894 133,688,157
7hr 125ppb 782,889 108,649,732
7hr 125ppb 782,889 108,753,400
7hr 225ppb 1,136,945 155,270,331
7hr 225ppb 1,136,945 155,379,747
7hr 80ppb 1,088,005 151,193,251
7hr 80ppb 1,088,005 151,359,381
7hr Control 1,126,105 157,898,477
7hr Control 1,126,105 157,983,421
TOTAL 16,853,408 2,307,273,959
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