Overview
Analysis Namede novo Black Walnut (Juglans nigra)
Transcriptome NameJuglans nigra 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 Contigs78,834
OrganismsJuglans nigra

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 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 - 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 Description Library Code Platform MiSeq Reads MiSeq Bases
Black Walnut female flowers BW M-29: Black Walnut female flowers Illumina MiSeq 721,567 206,947,969
Black Walnut catkins (male flowers-immature/not shed polen yet BW M-28: Black Walnut catkins (male flowers-immature/not shed polen yet Illumina MiSeq 719,895 207,499,385
Black Walnut green twigs/buds-this year growth BW M-24: Black Walnut green twigs/buds-this year growth Illumina MiSeq 880,029 253,297,039
Black Walnut damaged twigs BW M-23: Black Walnut damaged twigs Illumina MiSeq 675,671 194,450,127
Black Walnut undamaged twigs BW M-22: Black Walnut undamaged twigs Illumina MiSeq 675,126 195,626,822
Black Walnut damaged leaves BW M-21: Black Walnut damaged leaves Illumina MiSeq 368,792 104,807,057
Black Walnut undamaged leaves BW M-20: Black Walnut undamaged leaves Illumina MiSeq 738,015 209,603,847
Black Walnut dormant twigs BW M-19: Black Walnut dormant twigs Illumina MiSeq 698,063 199,435,213
Black Walnut catkins (male flowers- very mature) BW D-28: Black Walnut catkins (male flowers- very mature) Illumina MiSeq 682,678 195,440,232
Black Walnut green twigs/buds-this year growth BW D-24: Black Walnut green twigs/buds-this year growth Illumina MiSeq 740,491 213,298,767
Black Walnut damaged twigs BW D-23: Black Walnut damaged twigs Illumina MiSeq 649,989 186,988,159
Black Walnut undamaged twigs BW D-22: Black Walnut undamaged twigs Illumina MiSeq 736,100 211,143,703
Black Walnut damaged leaves Black Walnut damaged leaves Illumina MiSeq 530,530 153,416,149
Black Walnut undamaged leaves BW D-20: Black Walnut undamaged leaves Illumina MiSeq 669,077 192,127,827
Black Walnut dormant twigs BW D-19: Black Walnut dormant twigs Illumina MiSeq 759,331 217,047,889
Black Walnut control chamber ozone 10ppb 7hr BW-CH9-7hr: Black Walnut control chamber ozone 10ppb 7hr Illumina MiSeq 222,629 67,233,958
Black Walnut control chamber ozone 10ppb day 28 BW-CH9-28D: Black Walnut control chamber ozone 10ppb day 28 Illumina MiSeq 220,183 66,495,266
Black Walnut control chamber ozone 10ppb day14 BW-CH9-14D: Black Walnut control chamber ozone 10ppb day14 Illumina MiSeq 225,002 67,950,604
Black Walnut ozone exposure 225ppb for 7 hours BW-CH12-7hr: Black Walnut ozone exposure 225ppb for 7 hours Illumina MiSeq 207,588 62,691,576
Black Walnut ozone exposure 225ppb for 28 days BW-CH12-28D: Black Walnut ozone exposure 225ppb for 28 days Illumina MiSeq 228,796 69,096,392
Black Walnut ozone exposure 225ppb for 14 days BW-CH12-14D: Black Walnut ozone exposure 225ppb for 14 days Illumina MiSeq 226,216 68,317,232
Black Walnut ozone exposure 125ppb for 7 hours BW-CH11-7hr: Black Walnut ozone exposure 125ppb for 7 hours Illumina MiSeq 278,678 84,160,756
Black Walnut ozone exposure 125ppb for 28 days BW-CH11-28D: Black Walnut ozone exposure 125ppb for 28 days Illumina MiSeq 273,992 82,745,584
Black Walnut ozone exposure 125ppb for 14 days BW-CH11-14D: Black Walnut ozone exposure 125ppb for 14 days Illumina MiSeq 264,296 79,817,392
Black Walnut ozone exposure 80ppb for 7 hours BW-CH10-7hr: Black Walnut ozone exposure 80ppb for 7 hours Illumina MiSeq 238,840 72,129,680
Black Walnut ozone exposure 80ppb for 28 days BW-CH10-28D: Black Walnut ozone exposure 80ppb for 28 days Illumina MiSeq 191,811 57,926,922
Black Walnut ozone exposure 80ppb for 14 days BW-CH10-14D: Black Walnut ozone exposure 80ppb for 14 days Illumina MiSeq 248,995 75,196,490
Black Walnut Leaf, ozone28day+ hole punched, 0ppb BW OW-9: Black Walnut Leaf, ozone28day+ hole punched, 0ppb Illumina MiSeq 710,989 204,438,746
Black Walnut Leaf, ozone28day+ hole punched, 225ppb BW OW-12: Black Walnut Leaf, ozone28day+ hole punched, 225ppb Illumina MiSeq 716,200 204,246,072
Black Walnut Leaf, ozone28day+ hole punched, 125ppb BW OW-11: Black Walnut Leaf, ozone28day+ hole punched, 125ppb Illumina MiSeq 699,282 202,256,668
Black Walnut Leaf, ozone28day+ hole punched, 80ppb BW OW-10: Black Walnut Leaf, ozone28day+ hole punched, 80ppb Illumina MiSeq 698,725 201,727,333
TOTAL 15,897,576 4,607,560,856

Illumina HiSeq 2000 Data

Scroll up forMiSeq Data

Library Description Library Code Platform HiSeq Reads HiSeq Bases
Black Walnut female flowers BW M-29: Black Walnut female flowers Illumina HiSeq 2000 12,633,694 2,552,006,188
Black Walnut catkins (male flowers-immature/not shed polen yet BW M-28: Black Walnut catkins (male flowers-immature/not shed polen yet Illumina HiSeq 2000 12,677,603 2,560,875,806
Black Walnut green twigs/buds-this year growth BW M-24: Black Walnut green twigs/buds-this year growth Illumina HiSeq 2000 15,356,666 3,102,046,532
Black Walnut damaged twigs BW M-23: Black Walnut damaged twigs Illumina HiSeq 2000 10,080,608 2,036,282,816
Black Walnut undamaged twigs BW M-22: Black Walnut undamaged twigs Illumina HiSeq 2000 11,340,510 2,290,783,020
Black Walnut damaged leaves BW M-21: Black Walnut damaged leaves Illumina HiSeq 2000 7,098,053 1,433,806,706
Black Walnut undamaged leaves BW M-20: Black Walnut undamaged leaves Illumina HiSeq 2000 12,668,778 2,559,093,156
Black Walnut dormant twigs BW M-19: Black Walnut dormant twigs Illumina HiSeq 2000 10,217,418 2,063,918,436
Black Walnut catkins (male flowers- very mature) BW D-28: Black Walnut catkins (male flowers- very mature) Illumina HiSeq 2000 11,316,402 2,285,913,204
Black Walnut green twigs/buds-this year growth BW D-24: Black Walnut green twigs/buds-this year growth Illumina HiSeq 2000 11,098,321 2,241,860,842
Black Walnut damaged twigs BW D-23: Black Walnut damaged twigs Illumina HiSeq 2000 11,185,638 2,259,498,876
Black Walnut undamaged twigs BW D-22: Black Walnut undamaged twigs Illumina HiSeq 2000 11,315,803 2,285,792,206
Black Walnut damaged leaves BW D-21: Black Walnut damaged leaves Illumina HiSeq 2000 11,793,802 2,382,348,004
Black Walnut undamaged leaves BW D-20: Black Walnut undamaged leaves Illumina HiSeq 2000 11,465,348 2,316,000,296
Black Walnut dormant twigs BW D-19: Black Walnut dormant twigs Illumina HiSeq 2000 10,734,907 2,168,451,214
Black Walnut Leaf, ozone28day+ hole punched, 0ppb BW OW-9: Black Walnut Leaf, ozone28day+ hole punched, 0ppb Illumina HiSeq 2000 9,768,085 1,973,153,170
Black Walnut Leaf, ozone28day+ hole punched, 225ppb BW OW-12: Black Walnut Leaf, ozone28day+ hole punched, 225ppb Illumina HiSeq 2000 12,257,857 2,476,087,114
Black Walnut Leaf, ozone28day+ hole punched, 125ppb BW OW-11: Black Walnut Leaf, ozone28day+ hole punched, 125ppb Illumina HiSeq 2000 9,615,955 1,942,422,910
Black Walnut Leaf, ozone28day+ hole punched, 80ppb BW OW-10: Black Walnut Leaf, ozone28day+ hole punched, 80ppb Illumina HiSeq 2000 11,534,904 2,330,050,608
TOTAL 214,160,352 43,260,391,104
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