Overview
Analysis Namede novo Blackgum (Nyssa sylvatica)
Transcriptome NameNyssa sylvatica 101314
MethodTrinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST (trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27)
Source (101314)
Date performed2014-10-13
Number of Contigs138,819
OrganismsNyssa sylvatica

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 Transcripts 138,819
Transcript N50 1,039 bp
Transcript Average Length 570 bp
Number of Proteins 41,757
Protein N50 358 aa
Protein Average Length 285 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 Description Library Code Platform MiSeq Reads MiSeq Bases
Black Gum 29Day-80ppb BG-29Day-80_3 Illumina MiSeq 1,315,702 356,792,669
Black Gum 29Day-125ppb BG-29Day-125_2 Illumina MiSeq 1,400,948 382,078,889
Black Gum 29Day-control BG-29Day-CO_1 Illumina MiSeq 1,363,529 372,684,241
Black Gum 7HR-control BG-7HR-Co Illumina MiSeq 1,126,105 315,881,898
Black Gum 7HR-80ppb BG-7HR-80ppb Illumina MiSeq 1,088,005 302,552,632
Black Gum 7HR-225ppb BG-7HR-225ppb Illumina MiSeq 1,136,945 310,650,078
Black Gum 7HR-125ppb BG-7HR-125ppb Illumina MiSeq 782,889 217,403,132
Black Gum 29Day-control BG-29Day-CO Illumina MiSeq 1,264,501 380,121,712
Black Gum 29Day-80ppb BG-29Day-80 Illumina MiSeq 2,125,411 632,794,517
Black Gum 29Day-225ppb BG-29Day-225 Illumina MiSeq 1,350,371 377,609,658
Black Gum 29Day-125ppb BG-29Day-125 Illumina MiSeq 1,175,260 348,177,851
Black Gum 28Day-control BG-28Day-CO Illumina MiSeq 1,055,701 294,020,982
Black Gum 28Day-80ppb BG-28Day-80 Illumina MiSeq 1,159,053 322,402,420
Black Gum 28Day-225ppb BG-28Day-225 Illumina MiSeq 1,190,894 324,073,055
Black Gum 28Day-125ppb BG-28Day-125 Illumina MiSeq 983,260 274,602,203
Black Gum 14DAy-control BG-14DAy-Co Illumina MiSeq 959,894 267,277,864
Black Gum 14DAy-80ppb BG-14DAy-80ppb Illumina MiSeq 1,159,659 316,227,264
Black Gum 14DAy-225ppb BG-14DAy-225ppb Illumina MiSeq 1,210,565 317,659,432
Black Gum 14DAy-125ppb BG-14DAy-125ppb Illumina MiSeq 962,642 259,621,659
TOTAL 22,811,334 6,372,632,156
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