Overview
Analysis Namede novo Blackgum (Nyssa sylvatica) - 120313
Transcriptome NameNyssa sylvatica 120313
MethodTrinity; CD-HIT-EST (trinityrnaseq_r2013-11-10, cd-hit-v4.6.1-2012-08-27)
Source (120313)
Date performed2013-12-03
Number of Contigs55,630

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 Transcripts 55,630
Transcript N50 1,172 bp
Transcript Average Length 760 bp
Number of Proteins 30,838
Protein N50 338 aa
Protein Average Length 275 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 Description MiSeq Reads MiSeq 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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