Overview
Analysis Namede novo Northern Red Oak (Quercus rubra)
Transcriptome NameQuercus rubra 120313
MethodTrinity; CD-HIT-EST (trinityrnaseq_r2013_08_14, cd-hit-v4.6.1-2012-08-27)
Source (120313)
Date performed2013-12-03
Number of Contigs52,662
OrganismsQuercus rubra

Methods

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 Transcripts 78,834
Transcript N50 1,427 bp
Transcript Average Length 869 bp
Number of Proteins 42,665
Protein N50 365 aa
Protein Average Length 291 aa

Download assembled data:

Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

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 Description Library Code Platform 454 Reads 454 Bases
Red Oak above ground tissues ROA 454 GS FLX 131,630 32,102,277
Red Oak below ground tissues ROB 454 GS FLX 145,254 34,237,370
Red Oak ozone-300ppb sample D_21 454 GS FLX+ 261,387 135,955,675
Red Oak ozone-225ppb sample C_20 454 GS FLX+ 274,382 141,714,016
Red Oak ozone-150ppb sample B_19 454 GS FLX+ 302,634 155,961,285
Red Oak ozone-control sample A_18 454 GS FLX+ 266,500 139,583,352
TOTAL 1,382,057 639,553,975


Illumina MiSeq Data

Scroll down for HiSeq Data

Library Description Library Code Platform MiSeq Reads MiSeq Bases
Red Oak dormant twigs NRO D-4_84 Illumina MiSeq 473,211 134,102,510
Red Oak immature twig NRO D-39_83 Illumina MiSeq 767,235 221,393,115
Red Oak developing acorns NRO D-38_82 Illumina MiSeq 449,761 128,352,559
Red Oak undamaged twigs-late growth NRO D-37_81 Illumina MiSeq 524,976 149,740,370
Red Oak damaged twigs-late growth NRO D-36_80 Illumina MiSeq 238,386 67,335,954
Red Oak damaged leaves-late growth NRO D-2_79 Illumina MiSeq 341,686 97,170,091
Red Oak emerging leaf/bud NRO D-1_78 Illumina MiSeq 832,149 239,306,421
Red Oak catkin NRO M-4_77 Illumina MiSeq 522,677 150,009,358
Red Oak developing acorns NRO M-34_76 Illumina MiSeq 907,906 261,547,918
Red Oak undamaged twigs-late growth NRO M-33_75 Illumina MiSeq 955,659 275,587,195
Red Oak damaged twigs-late growth NRO M-32_74 Illumina MiSeq 384,410 111,527,035
Red Oak undamaged leaves-late growth NRO M-31_73 Illumina MiSeq 581,997 167,117,841
Red Oak damaged leaves-late growth NRO M-30_72 Illumina MiSeq 696,788 200,364,017
Red Oak immature twig NRO M-3_71 Illumina MiSeq 304,963 88,451,530
Red Oak emerging leaf/bud NRO M-2_70 Illumina MiSeq 340,834 97,682,283
Red Oak catkin NRO M-1_69 Illumina MiSeq 455,799 130,966,768
TOTAL 8,778,437 2,520,654,965



Illumina HiSeq 2000 and HiSeq 2500 Data

Scroll up forMiSeq Data

Library Description Library Code Platform HiSeq Reads HiSeq Bases
Red Oak O3-010ppb-control-07Hr. RO9-CO-7_68 Illumina HiSeq 2500 3,007,502 607,515,404
Red Oak O3-010ppb-control-28Day RO9-CO-28_67 Illumina HiSeq 2500 2,598,579 524,912,958
Red Oak O3-010ppb-control-14Day RO9-CO-14_66 Illumina HiSeq 2500 2,241,676 452,818,552
Red Oak O3-225ppb ozone-07Hr. RO8-225-7_65 Illumina HiSeq 2500 2,031,355 410,333,710
Red Oak O3-225ppb ozone-28Day RO8-225-28_64 Illumina HiSeq 2500 2,015,875 407,206,750
Red Oak O3-225ppb ozone-14Day RO8-225-14_63 Illumina HiSeq 2500 1,992,295 402,443,590
Red Oak O3-225ppb ozone-07Hr. RO7-225-7_62 Illumina HiSeq 2500 2,097,150 423,624,300
Red Oak O3-225ppb ozone-28Day RO7-225-28_61 Illumina HiSeq 2500 1,991,075 402,197,150
Red Oak O3-225ppb ozone-14Day RO7-225-14_60 Illumina HiSeq 2500 2,913,705 588,568,410
Red Oak O3-125ppb ozone-07Hr. RO6-125-7_59 Illumina HiSeq 2500 3,445,376 695,965,952
Red Oak O3-125ppb ozone-28Day RO6-125-28_58 Illumina HiSeq 2500 2,213,693 447,165,986
Red Oak O3-125ppb ozone-14Day RO6-125-14_57 Illumina HiSeq 2500 2,289,194 462,417,188
Red Oak O3-125ppb ozone-07Hr. RO5-125-7_56 Illumina HiSeq 2500 3,331,707 673,004,814
Red Oak O3-125ppb ozone-28Day RO5-125-28_55 Illumina HiSeq 2500 2,825,672 570,785,744
Red Oak O3-125ppb ozone-14Day RO5-125-14_54 Illumina HiSeq 2500 2,727,392 550,933,184
Red Oak O3-080ppb ozone-07Hr. RO4-80-7_53 Illumina HiSeq 2500 1,888,180 381,412,360
Red Oak O3-080ppb ozone-28Day RO4-80-28_52 Illumina HiSeq 2500 1,873,697 378,486,794
Red Oak O3-080ppb ozone-14Day RO4-80-14_51 Illumina HiSeq 2500 3,038,435 613,763,870
Red Oak O3-080ppb ozone-07Hr. RO3-80-7_50 Illumina HiSeq 2500 1,823,518 368,350,636
Red Oak O3-080ppb ozone-28Day RO3-80-28_49 Illumina HiSeq 2500 2,520,787 509,198,974
Red Oak O3-080ppb ozone-14Day RO3-80-14_48 Illumina HiSeq 2500 2,390,353 482,851,306
Red Oak O3-010ppb-control-07Hr. RO2-CO7_47 Illumina HiSeq 2500 2,423,165 489,479,330
Red Oak O3-010ppb-control-28Day RO2-CO28_46 Illumina HiSeq 2500 3,290,030 664,586,060
Red Oak O3-010ppb-control-14Day RO2-CO14_45 Illumina HiSeq 2500 2,268,157 458,167,714
Red Oak O3-010ppb-control-07Hr. RO1-CO7_44 Illumina HiSeq 2500 2,421,793 489,202,186
Red Oak O3-010ppb-control-28Day RO1-CO28_43 Illumina HiSeq 2500 2,357,601 476,235,402
Red Oak O3-010ppb-control-14Day RO1-CO-14_42 Illumina HiSeq 2500 2,753,590 556,225,180
Red Oak O3-225ppb ozone-07Hr. RO16-225-7_41 Illumina HiSeq 2500 3,013,150 608,656,300
Red Oak O3-225ppb ozone-28Day RO16-225-28_40 Illumina HiSeq 2500 2,060,201 416,160,602
Red Oak O3-225ppb ozone-14Day RO16-225-14_39 Illumina HiSeq 2500 1,891,124 382,007,048
Red Oak O3-225ppb ozone-07Hr. RO15-225-7_38 Illumina HiSeq 2500 2,038,681 411,813,562
Red Oak O3-225ppb ozone-28Day RO15-225-28_37 Illumina HiSeq 2500 2,642,553 533,795,706
Red Oak O3-225ppb ozone-14Day RO15-225-14_36 Illumina HiSeq 2500 1,915,241 386,878,682
Red Oak O3-125ppb ozone-07Hr. RO14-125-7_35 Illumina HiSeq 2500 2,138,999 432,077,798
Red Oak O3-125ppb ozone-28Day RO14-125-28_34 Illumina HiSeq 2500 3,126,708 631,595,016
Red Oak O3-125ppb ozone-07Hr. RO13-125-7_33 Illumina HiSeq 2500 2,276,151 459,782,502
Red Oak O3-125ppb ozone-28Day RO13-125-28_32 Illumina HiSeq 2500 2,169,693 438,277,986
Red Oak O3-125ppb ozone-14Day RO13-125-14_31 Illumina HiSeq 2500 2,105,987 425,409,374
Red Oak O3-080ppb ozone-07Hr. RO12-80-7_30 Illumina HiSeq 2500 2,350,311 474,762,822
Red Oak O3-080ppb ozone-28Day RO12-80-28_29 Illumina HiSeq 2500 2,874,056 580,559,312
Red Oak O3-080ppb ozone-14Day RO12-80-14_28 Illumina HiSeq 2500 2,846,081 574,908,362
Red Oak O3-080ppb ozone-07Hr. RO11-80-7_27 Illumina HiSeq 2500 1,884,738 380,717,076
Red Oak O3-080ppb ozone-28Day RO11-80-28_26 Illumina HiSeq 2500 2,346,403 473,973,406
Red Oak O3-080ppb ozone-14Day RO11-80-14_25 Illumina HiSeq 2500 2,902,669 586,339,138
Red Oak O3-010ppb-control-07Hr. RO10_CO-7_24 Illumina HiSeq 2500 2,335,609 471,793,018
Red Oak O3-010ppb-control-28Day RO10_CO-28_23 Illumina HiSeq 2500 2,433,524 491,571,848
Red Oak O3-010ppb-control-14Day RO10_CO-14_22 Illumina HiSeq 2500 2,336,242 471,920,884
Red Oak dormant twigs NRO D-4_17 Illumina HiSeq 2000 11,387,168 2,300,207,936
Red Oak immature twig NRO D-39_16 Illumina HiSeq 2000 17,286,746 3,491,922,692
Red Oak developing acorns NRO D-38_15 Illumina HiSeq 2000 8,459,810 1,708,881,620
Red Oak undamaged twigs-late growth NRO D-37_14 Illumina HiSeq 2000 11,862,362 2,396,197,124
Red Oak damaged twigs-late growth NRO D-36_13 Illumina HiSeq 2000 4,826,799 975,013,398
Red Oak undamaged leaves-late growth NRO D-3_12 Illumina HiSeq 2000 15,744,685 3,180,426,370
Red Oak damaged leaves-late growth NRO D-2_11 Illumina HiSeq 2000 8,151,853 1,646,674,306
Red Oak emerging leaf/bud NRO D-1_10 Illumina HiSeq 2000 16,615,599 3,356,350,998
Red Oak catkin NRO M-4_9 Illumina HiSeq 2000 11,995,939 2,423,179,678
Red Oak developing acorns NRO M-34_8 Illumina HiSeq 2000 21,142,858 4,270,857,316
Red Oak undamaged twigs-late growth NRO M-33_7 Illumina HiSeq 2000 19,408,917 3,920,601,234
Red Oak damaged twigs-late growth NRO M-32_6 Illumina HiSeq 2000 11,256,030 2,273,718,060
Red Oak undamaged leaves-late growth NRO M-31_5 Illumina HiSeq 2000 13,417,085 2,710,251,170
Red Oak damaged leaves-late growth NRO M-30_4 Illumina HiSeq 2000 13,201,009 2,666,603,818
Red Oak immature twig NRO M-3_3 Illumina HiSeq 2000 8,035,161 1,623,102,522
Red Oak emerging leaf/bud NRO M-2_2 Illumina HiSeq 2000 7,822,194 1,580,083,188
Red Oak catkin NRO M-1_1 Illumina HiSeq 2000 8,839,447 1,785,568,294
TOTAL 323,913,335 65,430,493,670