Overview
Analysis Namede novo American sweetgum (Liquidambar styraciflua)
Transcriptome NameLiquidambar styraciflua 010515
MethodTrinity, built under bowtie-1.0.1 and samtools-1.1; CD-HIT-EST (trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27)
Sourcede novo assembly
Date performed2015-01-05
Number of Contigs127,406
OrganismsLiquidambar styraciflua

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 Transcripts 127,406
Transcript N50 1,724 bp
Transcript Average Length 975 bp
Number of Proteins 64,669
Protein N50 396 aa
Protein Average Length 307 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

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Library Description Library Code Platform HiSeq Reads HiSeq Bases
American Sweetgum Wounding_5hr_PETIOLE SGWND5P Illumina HiSeq 2500 3,646,914 736,676,628
American Sweetgum Wounding_5hr_LEAF SGWND5L Illumina HiSeq 2500 2,808,391 567,294,982
American Sweetgum Wounding_3hr_PETIOLE SGWND3P Illumina HiSeq 2500 3,187,433 643,861,466
American Sweetgum Wounding_3hr_LEAF SGWND3L Illumina HiSeq 2500 3,199,923 646,384,446
American Sweetgum Wounding_24hr_PETIOLE SGWND24P Illumina HiSeq 2500 3,359,683 678,655,966
American Sweetgum Wounding_24hr_LEAF SGWND24L Illumina HiSeq 2500 3,604,320 728,072,640
American Sweetgum Wounding_0hr_LEAF SGWND0L Illumina HiSeq 2500 3,309,887 668,597,174
American Sweetgum Heat_4hr_ROOT SGHEAT4R Illumina HiSeq 2500 3,093,803 624,948,206
American Sweetgum Heat_4hr_PETIOLE SGHEAT4P Illumina HiSeq 2500 2,765,512 558,633,424
American Sweetgum Heat_4hr_LEAF SGHEAT4L Illumina HiSeq 2500 2,374,056 479,559,312
American Sweetgum Heat_24hr_ROOT SGHEAT24R Illumina HiSeq 2500 3,227,027 651,859,454
American Sweetgum Heat_24hr_PETIOLE SGHEAT24P Illumina HiSeq 2500 2,767,765 559,088,530
American Sweetgum Heat_24hr_LEAF SGHEAT24L Illumina HiSeq 2500 2,469,102 498,758,604
American Sweetgum Drought_7 Day_ROOT SGDRHT7DR Illumina HiSeq 2500 2,839,024 573,482,848
American Sweetgum Drought_7 Day_PETIOLE SGDRHT7DP Illumina HiSeq 2500 2,747,343 554,963,286
American Sweetgum Drought_7 Day_LEAF SGDRHT7DL Illumina HiSeq 2500 2,208,248 446,066,096
American Sweetgum Drought_14 Day_ROOT SGDRHT14DR Illumina HiSeq 2500 2,352,891 475,283,982
American Sweetgum Drought_14 Day_PETIOLE SGDRHT14DP Illumina HiSeq 2500 2,893,477 584,482,354
American Sweetgum Drought_14 Day_LEAF SGDRHT14DL Illumina HiSeq 2500 3,091,114 624,405,028
American Sweetgum Control_B_ROOT SGCTRLBR Illumina HiSeq 2500 2,963,133 598,552,866
American Sweetgum Control_B_PETIOLE SGCTRLBP Illumina HiSeq 2500 2,783,089 562,183,978
American Sweetgum Control_B_LEAF SGCTRLBL Illumina HiSeq 2500 2,647,239 534,742,278
American Sweetgum Control_ROOT SGCTRLAR Illumina HiSeq 2500 2,537,334 512,541,468
American Sweetgum Control_PETIOLE SGCTRLAP Illumina HiSeq 2500 2,427,990 490,453,980
American Sweetgum Control_LEAF SGCTRLAL Illumina HiSeq 2500 2,919,293 589,697,186
American Sweetgum Cold_4hr_ROOT SGCOLD4R Illumina HiSeq 2500 2,554,008 515,909,616
American Sweetgum Cold_4hr_PETIOLE SGCOLD4P Illumina HiSeq 2500 2,578,578 520,872,756
American Sweetgum Cold_4hr_LEAF SGCOLD4L Illumina HiSeq 2500 2,556,008 516,313,616
American Sweetgum Cold_24hr_ROOT SGCOLD24R Illumina HiSeq 2500 2,806,865 566,986,730
American Sweetgum Cold_24hr_PETIOLE SGCOLD24P Illumina HiSeq 2500 2,720,078 549,455,756
American Sweetgum Cold_24hr_LEAF SGCOLD24L Illumina HiSeq 2500 2,499,144 504,827,088
American Sweetgum O3-010ppb-control-07 Hr. SG-CO-7 Illumina HiSeq 2500 2,673,021 539,950,242
American Sweetgum O3-010ppb-control-28 Day SG-CO-28 Illumina HiSeq 2500 2,433,307 491,528,014
American Sweetgum O3-010ppb-control-14 Day SG-CO-14 Illumina HiSeq 2500 2,953,269 596,560,338
American Sweetgum O3-080ppb ozone-07 Hr. SG-80-7 Illumina HiSeq 2500 2,609,812 527,182,024
American Sweetgum O3-080ppb ozone-28 Day SG-80-28 Illumina HiSeq 2500 1,909,617 385,742,634
American Sweetgum O3-080ppb ozone-14 Day SG-80-14 Illumina HiSeq 2500 3,615,050 730,240,100
American Sweetgum O3-225ppb ozone-07 Hr. SG-225-7 Illumina HiSeq 2500 1,975,354 399,021,508
American Sweetgum O3-225ppb ozone-28 Day SG-225-28 Illumina HiSeq 2500 2,376,884 480,130,568
American Sweetgum O3-225ppb ozone-14 Day SG-225-14 Illumina HiSeq 2500 4,025,465 813,143,930
American Sweetgum O3-125ppb ozone-07 Hr. SG-125-7 Illumina HiSeq 2500 2,526,711 510,395,622
American Sweetgum O3-125ppb ozone-28 Day SG-125-28 Illumina HiSeq 2500 2,050,112 414,122,624
American Sweetgum O3-125ppb ozone-14 Day SG-125-14 Illumina HiSeq 2500 2,590,324 523,245,448
TOTAL 119,677,598 24,174,874,796

Illumina MiSeq Data

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The following library was not used in the assembly but was used for expression analysis.

Library Description Library Code Platform MiSeq Reads MiSeq Bases
Sweetgum - pooled seedling leaf RNAs from various stress treatments (round 1, round 2) SG1 Illumina MiSeq 1994506 525578470
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