Summary
Name
Nyssa sylvatica - Transcriptome Assembly
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
: 101314
Date Performed
Sunday, October 12, 2014 - 21:00
Number of transcripts
138819
Average Transcript Length
570
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 19 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 Transcripts138,819
Transcript N501,039 bp
Transcript Average Length570 bp
Number of Proteins41,757
Protein N50358 aa
Protein Average Length285 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 28% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 71% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 38% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 93% of proteins matched a Trembl plant entry
SSR Pipeline
Excel file with statistics, SSR motifs and primers (854 predicted high quality markers)

Read Statistics

RNA was sampled from leaves of seedlings exposed to ozone levels (control, 80ppm, 125ppm, or 225ppm) for 7 hours, 14 days, 28 days, 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
Black Gum 29Day-80ppbBG-29Day-80_3Illumina MiSeq1,315,702356,792,669
Black Gum 29Day-125ppbBG-29Day-125_2Illumina MiSeq1,400,948382,078,889
Black Gum 29Day-controlBG-29Day-CO_1Illumina MiSeq1,363,529372,684,241
Black Gum 7HR-controlBG-7HR-CoIllumina MiSeq1,126,105315,881,898
Black Gum 7HR-80ppbBG-7HR-80ppbIllumina MiSeq1,088,005302,552,632
Black Gum 7HR-225ppbBG-7HR-225ppbIllumina MiSeq1,136,945310,650,078
Black Gum 7HR-125ppbBG-7HR-125ppbIllumina MiSeq782,889217,403,132
Black Gum 29Day-controlBG-29Day-COIllumina MiSeq1,264,501380,121,712
Black Gum 29Day-80ppbBG-29Day-80Illumina MiSeq2,125,411632,794,517
Black Gum 29Day-225ppbBG-29Day-225Illumina MiSeq1,350,371377,609,658
Black Gum 29Day-125ppbBG-29Day-125Illumina MiSeq1,175,260348,177,851
Black Gum 28Day-controlBG-28Day-COIllumina MiSeq1,055,701294,020,982
Black Gum 28Day-80ppbBG-28Day-80Illumina MiSeq1,159,053322,402,420
Black Gum 28Day-225ppbBG-28Day-225Illumina MiSeq1,190,894324,073,055
Black Gum 28Day-125ppbBG-28Day-125Illumina MiSeq983,260274,602,203
Black Gum 14DAy-controlBG-14DAy-CoIllumina MiSeq959,894267,277,864
Black Gum 14DAy-80ppbBG-14DAy-80ppbIllumina MiSeq1,159,659316,227,264
Black Gum 14DAy-225ppbBG-14DAy-225ppbIllumina MiSeq1,210,565317,659,432
Black Gum 14DAy-125ppbBG-14DAy-125ppbIllumina MiSeq962,642259,621,659
TOTAL22,811,3346,372,632,156
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