Summary
Name
Liquidambar styraciflua - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Data Source
Source Name
: de novo assembly
Date Performed
Sunday, January 4, 2015 - 20:00
Number of transcripts
127406
Average Transcript Length
975
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
Description and Download
Description: 
This project aims to elucidate the molecular response of hardwood tree seedlings to heat, cold, drought, mechanical wounding, and 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 86 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 Transcripts127,406
Transcript N501,724 bp
Transcript Average Length975 bp
Number of Proteins64,669
Protein N50396 aa
Protein Average Length307 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 41% 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 - 53% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 89% of proteins matched a Trembl plant entry
SSR Pipeline
Excel file with statistics, SSR motifs and primers (2147 predicted high quality markers)

Read Statistics

RNA was sampled from leaves of seedlings exposed to ozone levels (control, 10ppm, 80ppm, 125ppm, or 225ppm) for 7 hours, 14 days, and 28 days. Leaf, petiole, and root samples were also taken from seedlings exposed to control, cold (4 hours, 24 hours), heat (4 hours, 24 hours), drought (7 days, 14 days), and wounding (0 hours, 3 hours, 5 hours, 24 hours). Raw data has been uploaded to the NCBI Short Read Archive. An additional MiSeq library (SG1) was not used in the assembly but was used in expression analysis. Links are included below.

Illumina HiSeq 2500 Data

Scroll down for MiSeq Data
Library DescriptionLibrary CodePlatformHiSeq ReadsHiSeq Bases
American Sweetgum Wounding_5hr_PETIOLESGWND5PIllumina HiSeq 25003,646,914736,676,628
American Sweetgum Wounding_5hr_LEAFSGWND5LIllumina HiSeq 25002,808,391567,294,982
American Sweetgum Wounding_3hr_PETIOLESGWND3PIllumina HiSeq 25003,187,433643,861,466
American Sweetgum Wounding_3hr_LEAFSGWND3LIllumina HiSeq 25003,199,923646,384,446
American Sweetgum Wounding_24hr_PETIOLESGWND24PIllumina HiSeq 25003,359,683678,655,966
American Sweetgum Wounding_24hr_LEAFSGWND24LIllumina HiSeq 25003,604,320728,072,640
American Sweetgum Wounding_0hr_LEAFSGWND0LIllumina HiSeq 25003,309,887668,597,174
American Sweetgum Heat_4hr_ROOTSGHEAT4RIllumina HiSeq 25003,093,803624,948,206
American Sweetgum Heat_4hr_PETIOLESGHEAT4PIllumina HiSeq 25002,765,512558,633,424
American Sweetgum Heat_4hr_LEAFSGHEAT4LIllumina HiSeq 25002,374,056479,559,312
American Sweetgum Heat_24hr_ROOTSGHEAT24RIllumina HiSeq 25003,227,027651,859,454
American Sweetgum Heat_24hr_PETIOLESGHEAT24PIllumina HiSeq 25002,767,765559,088,530
American Sweetgum Heat_24hr_LEAFSGHEAT24LIllumina HiSeq 25002,469,102498,758,604
American Sweetgum Drought_7 Day_ROOTSGDRHT7DRIllumina HiSeq 25002,839,024573,482,848
American Sweetgum Drought_7 Day_PETIOLESGDRHT7DPIllumina HiSeq 25002,747,343554,963,286
American Sweetgum Drought_7 Day_LEAFSGDRHT7DLIllumina HiSeq 25002,208,248446,066,096
American Sweetgum Drought_14 Day_ROOTSGDRHT14DRIllumina HiSeq 25002,352,891475,283,982
American Sweetgum Drought_14 Day_PETIOLESGDRHT14DPIllumina HiSeq 25002,893,477584,482,354
American Sweetgum Drought_14 Day_LEAFSGDRHT14DLIllumina HiSeq 25003,091,114624,405,028
American Sweetgum Control_B_ROOTSGCTRLBRIllumina HiSeq 25002,963,133598,552,866
American Sweetgum Control_B_PETIOLESGCTRLBPIllumina HiSeq 25002,783,089562,183,978
American Sweetgum Control_B_LEAFSGCTRLBLIllumina HiSeq 25002,647,239534,742,278
American Sweetgum Control_ROOTSGCTRLARIllumina HiSeq 25002,537,334512,541,468
American Sweetgum Control_PETIOLESGCTRLAPIllumina HiSeq 25002,427,990490,453,980
American Sweetgum Control_LEAFSGCTRLALIllumina HiSeq 25002,919,293589,697,186
American Sweetgum Cold_4hr_ROOTSGCOLD4RIllumina HiSeq 25002,554,008515,909,616
American Sweetgum Cold_4hr_PETIOLESGCOLD4PIllumina HiSeq 25002,578,578520,872,756
American Sweetgum Cold_4hr_LEAFSGCOLD4LIllumina HiSeq 25002,556,008516,313,616
American Sweetgum Cold_24hr_ROOTSGCOLD24RIllumina HiSeq 25002,806,865566,986,730
American Sweetgum Cold_24hr_PETIOLESGCOLD24PIllumina HiSeq 25002,720,078549,455,756
American Sweetgum Cold_24hr_LEAFSGCOLD24LIllumina HiSeq 25002,499,144504,827,088
American Sweetgum O3-010ppb-control-07 Hr.SG-CO-7Illumina HiSeq 25002,673,021539,950,242
American Sweetgum O3-010ppb-control-28 DaySG-CO-28Illumina HiSeq 25002,433,307491,528,014
American Sweetgum O3-010ppb-control-14 DaySG-CO-14Illumina HiSeq 25002,953,269596,560,338
American Sweetgum O3-080ppb ozone-07 Hr.SG-80-7Illumina HiSeq 25002,609,812527,182,024
American Sweetgum O3-080ppb ozone-28 DaySG-80-28Illumina HiSeq 25001,909,617385,742,634
American Sweetgum O3-080ppb ozone-14 DaySG-80-14Illumina HiSeq 25003,615,050730,240,100
American Sweetgum O3-225ppb ozone-07 Hr.SG-225-7Illumina HiSeq 25001,975,354399,021,508
American Sweetgum O3-225ppb ozone-28 DaySG-225-28Illumina HiSeq 25002,376,884480,130,568
American Sweetgum O3-225ppb ozone-14 DaySG-225-14Illumina HiSeq 25004,025,465813,143,930
American Sweetgum O3-125ppb ozone-07 Hr.SG-125-7Illumina HiSeq 25002,526,711510,395,622
American Sweetgum O3-125ppb ozone-28 DaySG-125-28Illumina HiSeq 25002,050,112414,122,624
American Sweetgum O3-125ppb ozone-14 DaySG-125-14Illumina HiSeq 25002,590,324523,245,448
TOTAL119,677,59824,174,874,796

Illumina MiSeq Data

Scroll up for HiSeq Data The following library was not used in the assembly but was used for expression analysis.
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Sweetgum - pooled seedling leaf RNAs from various stress treatments (round 1, round 2)SG1Illumina MiSeq1994506525578470
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