Summary
Name
Acer saccharum - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Acer saccharum
Data Source
Source Name
: de novo assembly
Source Version
: 022416
Date Performed
Tuesday, February 23, 2016 - 20:00
Number of transcripts
117861
Average Transcript Length
945
Program, Pipeline, Workflow or Method Name
Trinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST
Program Version
trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27
Cross Reference
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 51 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 Transcripts117,861
Transcript N501,667 bp
Transcript Average Length945 bp
Number of Proteins67,537
Protein N50365 aa
Protein Average Length283 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 42% 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-5 cutoff - 55% of transcripts matched a Trembl plant entry
Blastp, 1e-5 cutoff - 88% of proteins matched a Trembl plant entry
HMMER search against Pfam database
Excel output of all hits
SSR Pipeline
Excel file with statistics, SSR motifs and primers (1514 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, 21 days, 32 days), and wounding (0 hours, 3 hours, 5 hours, 24 hours). Samples were also taken from various pooled materials. Raw data has been uploaded to the NCBI Short Read Archive. Links to NCBI are included below for both sugar maple HiSeq results and sugar maple MiSeq results.

Illumina HiSeq 2500 Data

Scroll down for MiSeq Data
Library DescriptionLibrary CodePlatformHiSeq ReadsHiSeq Bases
Sugar Maple Wounding_5hr_PETIOLESMWND5PIllumina HiSeq 25002,833,622572,391,644
Sugar Maple Wounding_5hr_LEAFSMWND5LIllumina HiSeq 25002,393,297483,445,994
Sugar Maple Wounding_3hr_PETIOLESMWND3PIllumina HiSeq 25002,547,590514,613,180
Sugar Maple Wounding_3hr_LEAFSMWND3LIllumina HiSeq 25002,590,965523,374,930
Sugar Maple Wounding_24hr_PETIOLESMW24PIllumina HiSeq 25003,111,319628,486,438
Sugar Maple Wounding_24hr_LEAFSMWD24LIllumina HiSeq 25003,026,472611,347,344
Sugar Maple Wounding_0hr_LEAFSMWND0LIllumina HiSeq 25002,658,691537,055,582
Sugar Maple Heat_4hr_ROOTSMHEAT4RIllumina HiSeq 25003,273,276661,201,752
Sugar Maple Heat_4hr_PETIOLESMHEAT4PIllumina HiSeq 25002,741,960553,875,920
Sugar Maple Heat_4hr_LEAFSMHEAT4LIllumina HiSeq 25002,924,056590,659,312
Sugar Maple Heat_24hr_ROOTSMHEAT24RIllumina HiSeq 25002,199,164444,231,128
Sugar Maple Heat_24hr_PETIOLESMHEAT24PIllumina HiSeq 25003,327,052672,064,504
Sugar Maple Heat_24hr_LEAFSMHEAT24LIllumina HiSeq 25002,399,593484,717,786
Sugar Maple Drought_7Day_ROOTSMDRHT7DRIllumina HiSeq 25002,678,852541,128,104
Sugar Maple Drought_7Day_PETIOLESMDRHT7DPIllumina HiSeq 25002,373,254479,397,308
Sugar Maple Drought_7Day_LEAFSMDRHT7DLIllumina HiSeq 25002,238,072452,090,544
Sugar Maple Drought_32Day_ROOTSMDRHT32DRIllumina HiSeq 25002,823,614570,370,028
Sugar Maple Drought_32Day_PETIOLESMDRHT32DPIllumina HiSeq 25002,606,244526,461,288
Sugar Maple Drought_32Day_LEAFSMDRHT32DLIllumina HiSeq 25002,357,534476,221,868
Sugar Maple Drought_21Day_ROOTSMDRHT21DRIllumina HiSeq 25002,697,529544,900,858
Sugar Maple Drought_21Day_PETIOLESMDRHT21DPIllumina HiSeq 25002,669,535539,246,070
Sugar Maple Drought_21Day_LEAFSMDRHT21DLIllumina HiSeq 25002,309,738466,567,076
Sugar Maple Control_B_ROOTSMCTRLBRIllumina HiSeq 25002,537,230512,520,460
Sugar Maple Control_B_PETIOLESMCTRLBPIllumina HiSeq 25003,411,175689,057,350
Sugar Maple Control_B_LEAFSMCTRLBLIllumina HiSeq 25002,239,027452,283,454
Sugar Maple Control_ROOTSMCTRLARIllumina HiSeq 25002,079,580420,075,160
Sugar Maple Control_PETIOLESMCTRLAPIllumina HiSeq 25002,278,065460,169,130
Sugar Maple Control_LEAFSMCTRLALIllumina HiSeq 25002,421,378489,118,356
Sugar Maple Cold_4hr_ROOTSMCOLD4RIllumina HiSeq 25003,563,093719,744,786
Sugar Maple Cold_4hr_PETIOLESMCOLD4PIllumina HiSeq 25002,439,155492,709,310
Sugar Maple Cold_4hr_LEAFSMCOLD4LIllumina HiSeq 25002,531,863511,436,326
Sugar Maple Cold_24hr_ROOTSMCOLD24RIllumina HiSeq 25002,039,653412,009,906
Sugar Maple Cold_24hr_PETIOLESMCOLD24PIllumina HiSeq 25002,580,686521,298,572
Sugar Maple Cold_24hr_LEAFSMCOLD24LIllumina HiSeq 25002,447,647494,424,694
Sugar Maple O3-010ppb-control-07 Hr.SM-CO-7Illumina HiSeq 25002,867,230579,180,460
Sugar Maple O3-010ppb-control-28 DaySM-CO-28Illumina HiSeq 25003,204,564647,321,928
Sugar Maple O3-010ppb-control-14 DaySM-CO-14Illumina HiSeq 25002,698,654545,128,108
Sugar Maple O3-080ppb ozone-07 Hr.SM-80-7Illumina HiSeq 25002,454,451495,799,102
Sugar Maple O3-080ppb ozone-28 DaySM-80-28Illumina HiSeq 25002,623,628529,972,856
Sugar Maple O3-080ppb ozone-14 DaySM-80-14Illumina HiSeq 25002,295,384463,667,568
Sugar Maple O3-225ppb ozone-07 Hr.SM-225-7Illumina HiSeq 25002,750,677555,636,754
Sugar Maple O3-225ppb ozone-28 DaySM-225-28Illumina HiSeq 25002,116,424427,517,648
Sugar Maple O3-225ppb ozone-14 DaySM-225-14Illumina HiSeq 25003,348,468676,390,536
Sugar Maple O3-125ppb ozone-07 Hr.SM-125-7Illumina HiSeq 25002,736,309552,734,418
Sugar Maple O3-125ppb ozone-28 DaySM-125-28Illumina HiSeq 25003,516,187710,269,774
Sugar Maple O3-125ppb ozone-14 DaySM-125-14Illumina HiSeq 25002,589,137523,005,674
TOTAL122,551,09424,755,320,988

Illumina MiSeq Data

Scroll up for HiSeq Data
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Sugar Maple - pooled seedling leaf RNAs, 125 ppb ozoneSM125Illumina MiSeq43498881174821152
Sugar Maple - pooled seedling leaf RNAs, 225 ppb ozoneSM225Illumina MiSeq46474461245227243
Sugar Maple - pooled seedling leaf RNAs, 80 ppb ozoneSM80Illumina MiSeq41131151082886681
Sugar Maple - pooled seedling leaf RNAs, controlSMCOIllumina MiSeq42286931160544940
Sugar Maple - pooled seedling leaf RNAs from various stress treatments (round 1, round 2)SM1Illumina MiSeq3519779954704667
TOTAL208589215618184683
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