Overview
Analysis Namede novo Tulip Poplar (Liriodendron tulipifera)
Transcriptome NameLiriodendron tulipifera 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 Contigs58,249
OrganismsLiriodendron tulipifera

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. Data has been uploaded to NCBI ( go to NCBI BioProject page).

Assembly Statistics

Number of Transcripts 58,249
Transcript N50 1,360 bp
Transcript Average Length 835 bp
Number of Proteins 31,347
Protein N50 378 aa
Protein Average Length 297 aa

Download assembled data:

Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:

Blastx, 1e-5 cutoff - 47% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 70% of proteins matched a swiss-prot entry

BLAST against the Trembl protein database, only plant entries:

Blastx, 1e-4 cutoff - 63% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 89% of proteins matched a Trembl plant entry

InterProScan search

Excel output

SSR Pipeline

Excel file with statistics, SSR motifs and primers (489 predicted high quality markers)

Read Statistics

RNA was sampled from leaves of seedlings exposed to ozone levels (control, 80ppm, 125ppm, or 225ppm) at 7 hours, 14 days, 28 days, and 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
Tulip Poplar 29Day 80ppb + mechanical wounding TP-29Day-80b Illumina MiSeq 308,295 83,923,357
Tulip Poplar 7hr Control TP-7HR-Co Illumina MiSeq 1,023,282 285,127,021
Tulip Poplar 7hr 80ppb TP-7HR-80ppb Illumina MiSeq 1,073,063 297,925,470
Tulip Poplar 7hr 225ppb TP-7HR-225ppb Illumina MiSeq 2,670 682,174
Tulip Poplar 7hr 125ppb TP-7HR-125ppb Illumina MiSeq 1,139,738 319,099,431
Tulip Poplar 29Day Control + mechanical wounding TP-29Day-CO Illumina MiSeq 1,226,283 342,140,055
Tulip Poplar 29Day 80ppb + mechanical wounding TP-29Day-80 Illumina MiSeq 1,489,683 403,528,313
Tulip Poplar 29Day 225ppb + mechanical wounding TP-29Day-225 Illumina MiSeq 1,514,523 419,972,720
Tulip Poplar 29Day 125ppb + mechanical wounding TP-29Day-125 Illumina MiSeq 1,241,972 345,692,911
Tulip Poplar 28Day Control TP-28Day-CO Illumina MiSeq 1,617,874 445,921,831
Tulip Poplar 28Day 80ppb TP-28Day-80 Illumina MiSeq 864,164 233,018,505
Tulip Poplar 28Day 225ppb TP-28Day-225 Illumina MiSeq 1,175,094 320,066,671
Tulip Poplar 28Day 125ppb TP-28Day-125 Illumina MiSeq 1,183,664 333,688,621
Tulip Poplar 14Day Control TP-14DAy-Co Illumina MiSeq 785,027 213,273,306
Tulip Poplar 14Day 80ppb TP-14DAy-80ppb Illumina MiSeq 731,463 195,163,223
Tulip Poplar 14Day 225ppb TP-14DAy-225ppb Illumina MiSeq 340,810 95,943,980
Tulip Poplar 14Day 125ppb TP-14DAy-125ppb Illumina MiSeq 682,722 187,819,053
TOTAL 16,400,327 4,522,986,642

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.

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