Overview
Analysis Namede novo Sugar Maple (Acer saccharum)
Transcriptome NameAcer saccharum 022416
MethodTrinity, built under bowtie-1.0.1 and samtools-0.1.19; CD-HIT-EST (trinityrnaseq_r20131110, cd-hit-v4.6.1-2012-08-27)
Source (022416)
Date performed2016-02-24
Number of Contigs117,861
OrganismsAcer saccharum

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 Transcripts 117,861
Transcript N50 1,667 bp
Transcript Average Length 945 bp
Number of Proteins 67,537
Protein N50 365 aa
Protein Average Length 283 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 Description Library Code Platform HiSeq Reads HiSeq Bases
Sugar Maple Wounding_5hr_PETIOLE SMWND5P Illumina HiSeq 2500 2,833,622 572,391,644
Sugar Maple Wounding_5hr_LEAF SMWND5L Illumina HiSeq 2500 2,393,297 483,445,994
Sugar Maple Wounding_3hr_PETIOLE SMWND3P Illumina HiSeq 2500 2,547,590 514,613,180
Sugar Maple Wounding_3hr_LEAF SMWND3L Illumina HiSeq 2500 2,590,965 523,374,930
Sugar Maple Wounding_24hr_PETIOLE SMW24P Illumina HiSeq 2500 3,111,319 628,486,438
Sugar Maple Wounding_24hr_LEAF SMWD24L Illumina HiSeq 2500 3,026,472 611,347,344
Sugar Maple Wounding_0hr_LEAF SMWND0L Illumina HiSeq 2500 2,658,691 537,055,582
Sugar Maple Heat_4hr_ROOT SMHEAT4R Illumina HiSeq 2500 3,273,276 661,201,752
Sugar Maple Heat_4hr_PETIOLE SMHEAT4P Illumina HiSeq 2500 2,741,960 553,875,920
Sugar Maple Heat_4hr_LEAF SMHEAT4L Illumina HiSeq 2500 2,924,056 590,659,312
Sugar Maple Heat_24hr_ROOT SMHEAT24R Illumina HiSeq 2500 2,199,164 444,231,128
Sugar Maple Heat_24hr_PETIOLE SMHEAT24P Illumina HiSeq 2500 3,327,052 672,064,504
Sugar Maple Heat_24hr_LEAF SMHEAT24L Illumina HiSeq 2500 2,399,593 484,717,786
Sugar Maple Drought_7Day_ROOT SMDRHT7DR Illumina HiSeq 2500 2,678,852 541,128,104
Sugar Maple Drought_7Day_PETIOLE SMDRHT7DP Illumina HiSeq 2500 2,373,254 479,397,308
Sugar Maple Drought_7Day_LEAF SMDRHT7DL Illumina HiSeq 2500 2,238,072 452,090,544
Sugar Maple Drought_32Day_ROOT SMDRHT32DR Illumina HiSeq 2500 2,823,614 570,370,028
Sugar Maple Drought_32Day_PETIOLE SMDRHT32DP Illumina HiSeq 2500 2,606,244 526,461,288
Sugar Maple Drought_32Day_LEAF SMDRHT32DL Illumina HiSeq 2500 2,357,534 476,221,868
Sugar Maple Drought_21Day_ROOT SMDRHT21DR Illumina HiSeq 2500 2,697,529 544,900,858
Sugar Maple Drought_21Day_PETIOLE SMDRHT21DP Illumina HiSeq 2500 2,669,535 539,246,070
Sugar Maple Drought_21Day_LEAF SMDRHT21DL Illumina HiSeq 2500 2,309,738 466,567,076
Sugar Maple Control_B_ROOT SMCTRLBR Illumina HiSeq 2500 2,537,230 512,520,460
Sugar Maple Control_B_PETIOLE SMCTRLBP Illumina HiSeq 2500 3,411,175 689,057,350
Sugar Maple Control_B_LEAF SMCTRLBL Illumina HiSeq 2500 2,239,027 452,283,454
Sugar Maple Control_ROOT SMCTRLAR Illumina HiSeq 2500 2,079,580 420,075,160
Sugar Maple Control_PETIOLE SMCTRLAP Illumina HiSeq 2500 2,278,065 460,169,130
Sugar Maple Control_LEAF SMCTRLAL Illumina HiSeq 2500 2,421,378 489,118,356
Sugar Maple Cold_4hr_ROOT SMCOLD4R Illumina HiSeq 2500 3,563,093 719,744,786
Sugar Maple Cold_4hr_PETIOLE SMCOLD4P Illumina HiSeq 2500 2,439,155 492,709,310
Sugar Maple Cold_4hr_LEAF SMCOLD4L Illumina HiSeq 2500 2,531,863 511,436,326
Sugar Maple Cold_24hr_ROOT SMCOLD24R Illumina HiSeq 2500 2,039,653 412,009,906
Sugar Maple Cold_24hr_PETIOLE SMCOLD24P Illumina HiSeq 2500 2,580,686 521,298,572
Sugar Maple Cold_24hr_LEAF SMCOLD24L Illumina HiSeq 2500 2,447,647 494,424,694
Sugar Maple O3-010ppb-control-07 Hr. SM-CO-7 Illumina HiSeq 2500 2,867,230 579,180,460
Sugar Maple O3-010ppb-control-28 Day SM-CO-28 Illumina HiSeq 2500 3,204,564 647,321,928
Sugar Maple O3-010ppb-control-14 Day SM-CO-14 Illumina HiSeq 2500 2,698,654 545,128,108
Sugar Maple O3-080ppb ozone-07 Hr. SM-80-7 Illumina HiSeq 2500 2,454,451 495,799,102
Sugar Maple O3-080ppb ozone-28 Day SM-80-28 Illumina HiSeq 2500 2,623,628 529,972,856
Sugar Maple O3-080ppb ozone-14 Day SM-80-14 Illumina HiSeq 2500 2,295,384 463,667,568
Sugar Maple O3-225ppb ozone-07 Hr. SM-225-7 Illumina HiSeq 2500 2,750,677 555,636,754
Sugar Maple O3-225ppb ozone-28 Day SM-225-28 Illumina HiSeq 2500 2,116,424 427,517,648
Sugar Maple O3-225ppb ozone-14 Day SM-225-14 Illumina HiSeq 2500 3,348,468 676,390,536
Sugar Maple O3-125ppb ozone-07 Hr. SM-125-7 Illumina HiSeq 2500 2,736,309 552,734,418
Sugar Maple O3-125ppb ozone-28 Day SM-125-28 Illumina HiSeq 2500 3,516,187 710,269,774
Sugar Maple O3-125ppb ozone-14 Day SM-125-14 Illumina HiSeq 2500 2,589,137 523,005,674
TOTAL 122,551,094 24,755,320,988



Illumina MiSeq Data

Scroll up for HiSeq Data

Library Description Library Code Platform MiSeq Reads MiSeq Bases
Sugar Maple - pooled seedling leaf RNAs, 125 ppb ozone SM125 Illumina MiSeq 4349888 1174821152
Sugar Maple - pooled seedling leaf RNAs, 225 ppb ozone SM225 Illumina MiSeq 4647446 1245227243
Sugar Maple - pooled seedling leaf RNAs, 80 ppb ozone SM80 Illumina MiSeq 4113115 1082886681
Sugar Maple - pooled seedling leaf RNAs, control SMCO Illumina MiSeq 4228693 1160544940
Sugar Maple - pooled seedling leaf RNAs from various stress treatments (round 1, round 2) SM1 Illumina MiSeq 3519779 954704667
TOTAL 20858921 5618184683
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