Summary
Name
Juglans nigra - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Data Source
Source Name
: de novo assembly
Source Version
: 120313
Date Performed
Monday, December 2, 2013 - 20:00
Number of transcripts
78834
Average Transcript Length
869
Program, Pipeline, Workflow or Method Name
Trinity; CD-HIT-EST
Program Version
trinityrnaseq_r2013_08_14, cd-hit-v4.6.1-2012-08-27
Cross Reference
Description and Download
Description: 
MiSeq reads from multiple 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 Transcripts78,834
Transcript N501,427 bp
Transcript Average Length869 bp
Number of Proteins42,665
Protein N50365 aa
Protein Average Length291 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 49% 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-4 cutoff - 69% of transcripts matched a trembl entry
Blastp, 1e-5 cutoff - 94% 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
SSR Pipeline
Excel file with statistics, SSR motifs and primers (939 high quality markers)

Read Statistics

RNA was isolated and sequenced from a variety of tissues. Many of the tissues were from the mother (library code with an M) or the father (library code with a D) of the mapping population. Ozone stress and leaf punches assays were conducted on seedlings. Over 460 million reads 47.8Gb of sequence were acquired.
Raw ozone data is available from the previous assembly. Links to the short read archive of NCBI are included below for both black walnut MiSeq results and black walnut HiSeq results.

Illumina MiSeq Data

Scroll down for HiSeq Data
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Black Walnut female flowersBW M-29: Black Walnut female flowersIllumina MiSeq721,567206,947,969
Black Walnut catkins (male flowers-immature/not shed polen yetBW M-28: Black Walnut catkins (male flowers-immature/not shed polen yetIllumina MiSeq719,895207,499,385
Black Walnut green twigs/buds-this year growthBW M-24: Black Walnut green twigs/buds-this year growthIllumina MiSeq880,029253,297,039
Black Walnut damaged twigsBW M-23: Black Walnut damaged twigsIllumina MiSeq675,671194,450,127
Black Walnut undamaged twigsBW M-22: Black Walnut undamaged twigsIllumina MiSeq675,126195,626,822
Black Walnut damaged leavesBW M-21: Black Walnut damaged leavesIllumina MiSeq368,792104,807,057
Black Walnut undamaged leavesBW M-20: Black Walnut undamaged leavesIllumina MiSeq738,015209,603,847
Black Walnut dormant twigsBW M-19: Black Walnut dormant twigsIllumina MiSeq698,063199,435,213
Black Walnut catkins (male flowers- very mature)BW D-28: Black Walnut catkins (male flowers- very mature)Illumina MiSeq682,678195,440,232
Black Walnut green twigs/buds-this year growthBW D-24: Black Walnut green twigs/buds-this year growthIllumina MiSeq740,491213,298,767
Black Walnut damaged twigsBW D-23: Black Walnut damaged twigsIllumina MiSeq649,989186,988,159
Black Walnut undamaged twigsBW D-22: Black Walnut undamaged twigsIllumina MiSeq736,100211,143,703
Black Walnut damaged leavesBlack Walnut damaged leavesIllumina MiSeq530,530153,416,149
Black Walnut undamaged leavesBW D-20: Black Walnut undamaged leavesIllumina MiSeq669,077192,127,827
Black Walnut dormant twigsBW D-19: Black Walnut dormant twigsIllumina MiSeq759,331217,047,889
Black Walnut control chamber ozone 10ppb 7hrBW-CH9-7hr: Black Walnut control chamber ozone 10ppb 7hrIllumina MiSeq222,62967,233,958
Black Walnut control chamber ozone 10ppb day 28BW-CH9-28D: Black Walnut control chamber ozone 10ppb day 28Illumina MiSeq220,18366,495,266
Black Walnut control chamber ozone 10ppb day14BW-CH9-14D: Black Walnut control chamber ozone 10ppb day14Illumina MiSeq225,00267,950,604
Black Walnut ozone exposure 225ppb for 7 hoursBW-CH12-7hr: Black Walnut ozone exposure 225ppb for 7 hoursIllumina MiSeq207,58862,691,576
Black Walnut ozone exposure 225ppb for 28 daysBW-CH12-28D: Black Walnut ozone exposure 225ppb for 28 daysIllumina MiSeq228,79669,096,392
Black Walnut ozone exposure 225ppb for 14 daysBW-CH12-14D: Black Walnut ozone exposure 225ppb for 14 daysIllumina MiSeq226,21668,317,232
Black Walnut ozone exposure 125ppb for 7 hoursBW-CH11-7hr: Black Walnut ozone exposure 125ppb for 7 hoursIllumina MiSeq278,67884,160,756
Black Walnut ozone exposure 125ppb for 28 daysBW-CH11-28D: Black Walnut ozone exposure 125ppb for 28 daysIllumina MiSeq273,99282,745,584
Black Walnut ozone exposure 125ppb for 14 daysBW-CH11-14D: Black Walnut ozone exposure 125ppb for 14 daysIllumina MiSeq264,29679,817,392
Black Walnut ozone exposure 80ppb for 7 hoursBW-CH10-7hr: Black Walnut ozone exposure 80ppb for 7 hoursIllumina MiSeq238,84072,129,680
Black Walnut ozone exposure 80ppb for 28 daysBW-CH10-28D: Black Walnut ozone exposure 80ppb for 28 daysIllumina MiSeq191,81157,926,922
Black Walnut ozone exposure 80ppb for 14 daysBW-CH10-14D: Black Walnut ozone exposure 80ppb for 14 daysIllumina MiSeq248,99575,196,490
Black Walnut Leaf, ozone28day+ hole punched, 0ppbBW OW-9: Black Walnut Leaf, ozone28day+ hole punched, 0ppbIllumina MiSeq710,989204,438,746
Black Walnut Leaf, ozone28day+ hole punched, 225ppbBW OW-12: Black Walnut Leaf, ozone28day+ hole punched, 225ppbIllumina MiSeq716,200204,246,072
Black Walnut Leaf, ozone28day+ hole punched, 125ppbBW OW-11: Black Walnut Leaf, ozone28day+ hole punched, 125ppbIllumina MiSeq699,282202,256,668
Black Walnut Leaf, ozone28day+ hole punched, 80ppbBW OW-10: Black Walnut Leaf, ozone28day+ hole punched, 80ppbIllumina MiSeq698,725201,727,333
TOTAL15,897,5764,607,560,856

Illumina HiSeq 2000 Data

Scroll up forMiSeq Data
Library DescriptionLibrary CodePlatformHiSeq ReadsHiSeq Bases
Black Walnut female flowersBW M-29: Black Walnut female flowersIllumina HiSeq 200012,633,6942,552,006,188
Black Walnut catkins (male flowers-immature/not shed polen yetBW M-28: Black Walnut catkins (male flowers-immature/not shed polen yetIllumina HiSeq 200012,677,6032,560,875,806
Black Walnut green twigs/buds-this year growthBW M-24: Black Walnut green twigs/buds-this year growthIllumina HiSeq 200015,356,6663,102,046,532
Black Walnut damaged twigsBW M-23: Black Walnut damaged twigsIllumina HiSeq 200010,080,6082,036,282,816
Black Walnut undamaged twigsBW M-22: Black Walnut undamaged twigsIllumina HiSeq 200011,340,5102,290,783,020
Black Walnut damaged leavesBW M-21: Black Walnut damaged leavesIllumina HiSeq 20007,098,0531,433,806,706
Black Walnut undamaged leavesBW M-20: Black Walnut undamaged leavesIllumina HiSeq 200012,668,7782,559,093,156
Black Walnut dormant twigsBW M-19: Black Walnut dormant twigsIllumina HiSeq 200010,217,4182,063,918,436
Black Walnut catkins (male flowers- very mature)BW D-28: Black Walnut catkins (male flowers- very mature)Illumina HiSeq 200011,316,4022,285,913,204
Black Walnut green twigs/buds-this year growthBW D-24: Black Walnut green twigs/buds-this year growthIllumina HiSeq 200011,098,3212,241,860,842
Black Walnut damaged twigsBW D-23: Black Walnut damaged twigsIllumina HiSeq 200011,185,6382,259,498,876
Black Walnut undamaged twigsBW D-22: Black Walnut undamaged twigsIllumina HiSeq 200011,315,8032,285,792,206
Black Walnut damaged leavesBW D-21: Black Walnut damaged leavesIllumina HiSeq 200011,793,8022,382,348,004
Black Walnut undamaged leavesBW D-20: Black Walnut undamaged leavesIllumina HiSeq 200011,465,3482,316,000,296
Black Walnut dormant twigsBW D-19: Black Walnut dormant twigsIllumina HiSeq 200010,734,9072,168,451,214
Black Walnut Leaf, ozone28day+ hole punched, 0ppbBW OW-9: Black Walnut Leaf, ozone28day+ hole punched, 0ppbIllumina HiSeq 20009,768,0851,973,153,170
Black Walnut Leaf, ozone28day+ hole punched, 225ppbBW OW-12: Black Walnut Leaf, ozone28day+ hole punched, 225ppbIllumina HiSeq 200012,257,8572,476,087,114
Black Walnut Leaf, ozone28day+ hole punched, 125ppbBW OW-11: Black Walnut Leaf, ozone28day+ hole punched, 125ppbIllumina HiSeq 20009,615,9551,942,422,910
Black Walnut Leaf, ozone28day+ hole punched, 80ppbBW OW-10: Black Walnut Leaf, ozone28day+ hole punched, 80ppbIllumina HiSeq 200011,534,9042,330,050,608
TOTAL214,160,35243,260,391,104
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