Nyssa sylvatica - Transcriptome Assembly

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) Nyssa_sylvatica_10132014_transcripts.fasta
	Predicted ORFs (fasta format) Nyssa_sylvatica_10132014_peptide.fasta

Annotation

BLAST against the Swiss-prot protein database:

	Blastx, 1e-5 cutoff - 28% of transcripts matched a swiss-prot entry blackgum_sprot_nt.xlsx (Excel file with best hits)
	Blastp, 1e-5 cutoff - 71% of proteins matched a swiss-prot entry blackgum_sprot_aa.xlsx (Excel file with best hits)

BLAST against the Trembl protein database, only plant entries:

	Blastx, 1e-4 cutoff - 38% of transcripts matched a Trembl plant entry blackgum_blastx_trembl (Excel file with best hits)
	Blastp, 1e-5 cutoff - 93% of proteins matched a Trembl plant entry blackgum_trembl_aa.xlsx (Excel file with best hits)

SSR Pipeline

	Excel file with statistics, SSR motifs and primers (854 predicted high quality markers) Nyssa_sylvatica_10132014_transcripts.fasta.ssr_report.xlsx

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