Quercus rubra - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Data Source
Source Name
: de novo assembly
Source Version
: 120313
Date Performed
Monday, December 2, 2013 - 20:00
Number of transcripts
Average Transcript Length
Program, Pipeline, Workflow or Method Name
Trinity; CD-HIT-EST
Program Version
trinityrnaseq_r2013_08_14, cd-hit-v4.6.1-2012-08-27
Description and Download


Illumina MiSeq and Roche 454 reads were cleaned with Trimmomatic and assembled by Trinity. (Illumina HiSeq reads were used for expression analysis only). 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 Transcripts52,662
Transcript N501,244 bp
Transcript Average Length778 bp
Number of Proteins27,764
Protein N50368 aa
Protein Average Length293 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)


BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 51% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 73% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 48% of transcripts matched a trembl entry
Blastp, 1e-5 cutoff - 95% of proteins matched a trembl entry
HMMER search against Pfam database
Excel output of all hits
Proteins assigned to GO terms inferred from pfam hits
Simple Sequence Repeat (SSR) and Flanking Primer Identification
Excel file with statistics, SSR motifs and primers (497 high quality markers)

Libraries and Reads

Over 436 million reads and 44Gb of sequence were acquired. Tissues were from the mother (library code with an M) or the father (library code with a D) of the mapping population. Raw data has been uploaded to the NCBI Short Read Archive. Links are included below.

454 Data

Library DescriptionLibrary CodePlatform454 Reads454 Bases
Red Oak above ground tissuesROA454 GS FLX131,63032,102,277
Red Oak below ground tissuesROB454 GS FLX145,25434,237,370
Red Oak ozone-300ppbsample D_21454 GS FLX+261,387135,955,675
Red Oak ozone-225ppbsample C_20454 GS FLX+274,382141,714,016
Red Oak ozone-150ppbsample B_19454 GS FLX+302,634155,961,285
Red Oak ozone-controlsample A_18454 GS FLX+266,500139,583,352
TOTAL 1,382,057 639,553,975

Illumina MiSeq Data

Scroll down for HiSeq Data
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Red Oak dormant twigsNRO D-4_84Illumina MiSeq473,211134,102,510
Red Oak immature twigNRO D-39_83Illumina MiSeq767,235221,393,115
Red Oak developing acornsNRO D-38_82Illumina MiSeq449,761128,352,559
Red Oak undamaged twigs-late growthNRO D-37_81Illumina MiSeq524,976149,740,370
Red Oak damaged twigs-late growthNRO D-36_80Illumina MiSeq238,38667,335,954
Red Oak damaged leaves-late growthNRO D-2_79Illumina MiSeq341,68697,170,091
Red Oak emerging leaf/budNRO D-1_78Illumina MiSeq832,149239,306,421
Red Oak catkinNRO M-4_77Illumina MiSeq522,677150,009,358
Red Oak developing acornsNRO M-34_76Illumina MiSeq907,906261,547,918
Red Oak undamaged twigs-late growthNRO M-33_75Illumina MiSeq955,659275,587,195
Red Oak damaged twigs-late growthNRO M-32_74Illumina MiSeq384,410111,527,035
Red Oak undamaged leaves-late growthNRO M-31_73Illumina MiSeq581,997167,117,841
Red Oak damaged leaves-late growthNRO M-30_72Illumina MiSeq696,788200,364,017
Red Oak immature twigNRO M-3_71Illumina MiSeq304,96388,451,530
Red Oak emerging leaf/budNRO M-2_70Illumina MiSeq340,83497,682,283
Red Oak catkinNRO M-1_69Illumina MiSeq455,799130,966,768

Illumina HiSeq 2000 and HiSeq 2500 Data

Scroll up forMiSeq Data
Library DescriptionLibrary CodePlatformHiSeq ReadsHiSeq Bases
Red Oak O3-010ppb-control-07Hr.RO9-CO-7_68Illumina HiSeq 25003,007,502607,515,404
Red Oak O3-010ppb-control-28DayRO9-CO-28_67Illumina HiSeq 25002,598,579524,912,958
Red Oak O3-010ppb-control-14DayRO9-CO-14_66Illumina HiSeq 25002,241,676452,818,552
Red Oak O3-225ppb ozone-07Hr.RO8-225-7_65Illumina HiSeq 25002,031,355410,333,710
Red Oak O3-225ppb ozone-28DayRO8-225-28_64Illumina HiSeq 25002,015,875407,206,750
Red Oak O3-225ppb ozone-14DayRO8-225-14_63Illumina HiSeq 25001,992,295402,443,590
Red Oak O3-225ppb ozone-07Hr.RO7-225-7_62Illumina HiSeq 25002,097,150423,624,300
Red Oak O3-225ppb ozone-28DayRO7-225-28_61Illumina HiSeq 25001,991,075402,197,150
Red Oak O3-225ppb ozone-14DayRO7-225-14_60Illumina HiSeq 25002,913,705588,568,410
Red Oak O3-125ppb ozone-07Hr.RO6-125-7_59Illumina HiSeq 25003,445,376695,965,952
Red Oak O3-125ppb ozone-28DayRO6-125-28_58Illumina HiSeq 25002,213,693447,165,986
Red Oak O3-125ppb ozone-14DayRO6-125-14_57Illumina HiSeq 25002,289,194462,417,188
Red Oak O3-125ppb ozone-07Hr.RO5-125-7_56Illumina HiSeq 25003,331,707673,004,814
Red Oak O3-125ppb ozone-28DayRO5-125-28_55Illumina HiSeq 25002,825,672570,785,744
Red Oak O3-125ppb ozone-14DayRO5-125-14_54Illumina HiSeq 25002,727,392550,933,184
Red Oak O3-080ppb ozone-07Hr.RO4-80-7_53Illumina HiSeq 25001,888,180381,412,360
Red Oak O3-080ppb ozone-28DayRO4-80-28_52Illumina HiSeq 25001,873,697378,486,794
Red Oak O3-080ppb ozone-14DayRO4-80-14_51Illumina HiSeq 25003,038,435613,763,870
Red Oak O3-080ppb ozone-07Hr.RO3-80-7_50Illumina HiSeq 25001,823,518368,350,636
Red Oak O3-080ppb ozone-28DayRO3-80-28_49Illumina HiSeq 25002,520,787509,198,974
Red Oak O3-080ppb ozone-14DayRO3-80-14_48Illumina HiSeq 25002,390,353482,851,306
Red Oak O3-010ppb-control-07Hr.RO2-CO7_47Illumina HiSeq 25002,423,165489,479,330
Red Oak O3-010ppb-control-28DayRO2-CO28_46Illumina HiSeq 25003,290,030664,586,060
Red Oak O3-010ppb-control-14DayRO2-CO14_45Illumina HiSeq 25002,268,157458,167,714
Red Oak O3-010ppb-control-07Hr.RO1-CO7_44Illumina HiSeq 25002,421,793489,202,186
Red Oak O3-010ppb-control-28DayRO1-CO28_43Illumina HiSeq 25002,357,601476,235,402
Red Oak O3-010ppb-control-14DayRO1-CO-14_42Illumina HiSeq 25002,753,590556,225,180
Red Oak O3-225ppb ozone-07Hr.RO16-225-7_41Illumina HiSeq 25003,013,150608,656,300
Red Oak O3-225ppb ozone-28DayRO16-225-28_40Illumina HiSeq 25002,060,201416,160,602
Red Oak O3-225ppb ozone-14DayRO16-225-14_39Illumina HiSeq 25001,891,124382,007,048
Red Oak O3-225ppb ozone-07Hr.RO15-225-7_38Illumina HiSeq 25002,038,681411,813,562
Red Oak O3-225ppb ozone-28DayRO15-225-28_37Illumina HiSeq 25002,642,553533,795,706
Red Oak O3-225ppb ozone-14DayRO15-225-14_36Illumina HiSeq 25001,915,241386,878,682
Red Oak O3-125ppb ozone-07Hr.RO14-125-7_35Illumina HiSeq 25002,138,999432,077,798
Red Oak O3-125ppb ozone-28DayRO14-125-28_34Illumina HiSeq 25003,126,708631,595,016
Red Oak O3-125ppb ozone-07Hr.RO13-125-7_33Illumina HiSeq 25002,276,151459,782,502
Red Oak O3-125ppb ozone-28DayRO13-125-28_32Illumina HiSeq 25002,169,693438,277,986
Red Oak O3-125ppb ozone-14DayRO13-125-14_31Illumina HiSeq 25002,105,987425,409,374
Red Oak O3-080ppb ozone-07Hr.RO12-80-7_30Illumina HiSeq 25002,350,311474,762,822
Red Oak O3-080ppb ozone-28DayRO12-80-28_29Illumina HiSeq 25002,874,056580,559,312
Red Oak O3-080ppb ozone-14DayRO12-80-14_28Illumina HiSeq 25002,846,081574,908,362
Red Oak O3-080ppb ozone-07Hr.RO11-80-7_27Illumina HiSeq 25001,884,738380,717,076
Red Oak O3-080ppb ozone-28DayRO11-80-28_26Illumina HiSeq 25002,346,403473,973,406
Red Oak O3-080ppb ozone-14DayRO11-80-14_25Illumina HiSeq 25002,902,669586,339,138
Red Oak O3-010ppb-control-07Hr.RO10_CO-7_24Illumina HiSeq 25002,335,609471,793,018
Red Oak O3-010ppb-control-28DayRO10_CO-28_23Illumina HiSeq 25002,433,524491,571,848
Red Oak O3-010ppb-control-14DayRO10_CO-14_22Illumina HiSeq 25002,336,242471,920,884
Red Oak dormant twigsNRO D-4_17Illumina HiSeq 200011,387,1682,300,207,936
Red Oak immature twigNRO D-39_16Illumina HiSeq 200017,286,7463,491,922,692
Red Oak developing acornsNRO D-38_15Illumina HiSeq 20008,459,8101,708,881,620
Red Oak undamaged twigs-late growthNRO D-37_14Illumina HiSeq 200011,862,3622,396,197,124
Red Oak damaged twigs-late growthNRO D-36_13Illumina HiSeq 20004,826,799975,013,398
Red Oak undamaged leaves-late growthNRO D-3_12Illumina HiSeq 200015,744,6853,180,426,370
Red Oak damaged leaves-late growthNRO D-2_11Illumina HiSeq 20008,151,8531,646,674,306
Red Oak emerging leaf/budNRO D-1_10Illumina HiSeq 200016,615,5993,356,350,998
Red Oak catkinNRO M-4_9Illumina HiSeq 200011,995,9392,423,179,678
Red Oak developing acornsNRO M-34_8Illumina HiSeq 200021,142,8584,270,857,316
Red Oak undamaged twigs-late growthNRO M-33_7Illumina HiSeq 200019,408,9173,920,601,234
Red Oak damaged twigs-late growthNRO M-32_6Illumina HiSeq 200011,256,0302,273,718,060
Red Oak undamaged leaves-late growthNRO M-31_5Illumina HiSeq 200013,417,0852,710,251,170
Red Oak damaged leaves-late growthNRO M-30_4Illumina HiSeq 200013,201,0092,666,603,818
Red Oak immature twigNRO M-3_3Illumina HiSeq 20008,035,1611,623,102,522
Red Oak emerging leaf/budNRO M-2_2Illumina HiSeq 20007,822,1941,580,083,188
Red Oak catkinNRO M-1_1Illumina HiSeq 20008,839,4471,785,568,294
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