[Archived] Liriodendron tulipifera - Transcriptome Assembly v120313

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 seven 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	53,346
Transcript N50	1,237 bp
Transcript Average Length	749 bp
Number of Proteins	26,248
Protein N50	369 aa
Protein Average Length	292 aa

Download assembled data:

	Putative Transcripts (fasta format) Liriodendron_tulipifera_112213_transcripts.fasta
	Predicted ORFs (fasta format) Liriodendron_tulipifera_112213_proteins.fasta

Annotation

BLAST against the Swiss-prot protein database:

	Blastx, 1e-5 cutoff - 46% of transcripts matched a swiss-prot entry Excel file with best hits
	Blastp, 1e-5 cutoff - 69% of proteins matched a swiss-prot entry Excel file with best hits

BLAST against the Trembl protein database, only plant entries:

	Blastx, 1e-5 cutoff - 63% of transcripts matched a Trembl plant entry Excel file with best hits
	Blastp, 1e-5 cutoff - 91% of proteins matched a Trembl plant entry Excel file with best hits

HMMER search against Pfam database

	Excel output of all hits Liriodendron_tulipifera_120313_proteins-pFam.xlsx"
	Proteins assigned to GO terms inferred from pfam hits Liriodendron_tulipifera_120313_proteins-pFam-GOterms.xlsx

SSR Pipeline

	Excel file with statistics, SSR motifs and primers (388 predicted high quality markers) Liriodendron_tulipifera_120313_transcripts.fasta.ssr_report.xlsx
	Fasta file of sequences with an SSR repeat and primers (388 sequences) Liriodendron_tulipifera_120313_transcripts.fasta.ssr_filtered.fasta

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	682,722	93,967,711
14Day 225ppb	340,810	47,948,411
14Day 225ppb	340,810	47,995,569
14Day 80ppb	731,463	97,514,441
14Day 80ppb	731,463	97,648,782
14Day control	785,027	106,569,437
14Day control	785,027	106,703,869
7hr 125ppb	1,139,738	159,465,574
7hr 125ppb	1,139,738	159,633,857
7hr 225ppb	2,670	340,408
7hr 225ppb	2,670	341,766
7hr 80ppb	1,073,063	148,872,614
7hr 80ppb	1,073,063	149,052,856
7hr control	1,023,282	142,480,844
7hr control	1,023,282	142,646,177
TOTAL	11,557,550	1,595,033,658

In addition to the miSeq reads from the ozone experiments, two other sources of transcripts were used for the assembly. 2.3 million 454 reads from the ancestral genome project and 24,663 reads from the EST division of NCBI.