Summary
Name
Fraxinus pennsylvanica - Transcriptome Assembly
Resource Type
Transcriptome Assembly
Organism
Ontology Browser
View Gene Ontology browser or KEGG Ontology browser for Fraxinus pennsylvanica
Data Source
Source Name
: Fraxinus pennsylvanica 120313
Source Version
: 120313
Date Performed
Monday, December 2, 2013 - 20:00
Number of transcripts
107611
Average Transcript Length
818
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 Transcripts107,611
Transcript N501,327 bp
Transcript Average Length818 bp
Number of Proteins52,899
Protein N50352 aa
Protein Average Length285 aa
Download assembled data:
Putative Transcripts (fasta format)
Predicted ORFs (fasta format)

Annotation

BLAST against the Swiss-prot protein database:
Blastx, 1e-5 cutoff - 44% of transcripts matched a swiss-prot entry
Blastp, 1e-5 cutoff - 72% of proteins matched a swiss-prot entry
BLAST against the Trembl protein database, only plant entries:
Blastx, 1e-4 cutoff - 63% 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
SSR Pipeline
Excel file with statistics, SSR motifs and primers (484 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 953 million reads (98.7Gb) 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 green ash MiSeq results and green ash HiSeq results.

Illumina MiSeq Data

Scroll down for HiSeq Data
Library DescriptionLibrary CodePlatformMiSeq ReadsMiSeq Bases
Green Ash Leaf-controlGA-COL_13Illumina MiSeq679,517184,481,554
Green ash control chamber ozone 10ppbGA OW-9_53Illumina MiSeq352,040100,212,219
Green ash ozone exposure 225ppb for 29 day + mecanical wounding on day 28GA OW-12_52Illumina MiSeq352,289100,081,024
Green ash ozone exposure 125ppb for 29 day + mecanical wounding on day 28GA OW-11_51Illumina MiSeq306,84887,140,122
Green ash ozone exposure 80ppb for 29 day + mecanical wounding on day 28GA OW-10_50Illumina MiSeq344,50097,989,386
Green ash root heat (40C) exposure for 24hrGA-HR_49Illumina MiSeq379,593108,085,633
Green ash petiole heat (40C) exposure for 24hrGA-HP_48Illumina MiSeq383,170108,952,578
Green ash leaf heat (40C) exposure for 24hrGA-HL_47Illumina MiSeq399,220113,997,045
Green ash root drought(<1.0 mpa)GA-DR_46Illumina MiSeq562,139160,480,214
Green ash petiole drought(<1.0 mpa)GA-DP_45Illumina MiSeq584,023167,177,488
Green ash leaf drought(<1.0 mpa)GA-DL_44Illumina MiSeq660,912188,252,692
Green Ash root cold (4C) 0 time point controlGA-CR_43Illumina MiSeq575,597163,144,120
Green Ash petiole cold (4C) 0 time point controlGA-CP_42Illumina MiSeq531,475151,227,565
Green Ash leaf cold (4C) 0 time point controlGA-CL_41Illumina MiSeq485,738137,925,562
Green Ash root cold (4C) exposure for 24hr24-GA-CR_40Illumina MiSeq512,688146,651,958
Green Ash petiole cold (4C) exposure for 24hr24-GA-CP_39Illumina MiSeq438,573125,271,028
Green Ash leaf cold (4C) exposure for24hr24-GA-CL_38Illumina MiSeq1,802,378510,732,344
Green Ash terminal budsGA M-8_37Illumina MiSeq383,853109,745,634
Green Ash axial budsGA M-7_36Illumina MiSeq388,060110,648,513
Green Ash seed wingsGA M-6_35Illumina MiSeq2,016,332576,094,593
Green Ash 3 year old tissue for xilemGA M-5_34Illumina MiSeq2,393,054674,340,974
Green Ash damaged twigs-1 year oldGA M-4_33Illumina MiSeq456,291130,748,682
Green Ash undamaged twigs-1 year oldGA M-3_32Illumina MiSeq325,61192,780,707
Green Ash damaged leaflets-hole punchedGA M-2_31Illumina MiSeq428,915121,834,598
Green Ash undamaged leafletsGA M-1_30Illumina MiSeq361,217102,968,873
Green Ash FS-12, post-EAB (8 weeks after egg application)FS-12 egg_29Illumina MiSeq779,414215,297,514
Green Ash FS-10, post-EAB (8 weeks after egg application)FS-10 egg_28Illumina MiSeq779,311210,302,624
Green Ash FS-9, pre-EABFS-9_27Illumina MiSeq655,536179,802,000
Green Ash FS-8, post-EAB (8 weeks after egg application)FS-8 egg_26Illumina MiSeq671,151186,759,904
Green Ash FS-7, pre-EABFS-7_25Illumina MiSeq631,463174,071,104
Green Ash FS-6, post-EAB (8 weeks after egg application)FS-6 egg_24Illumina MiSeq635,956175,064,290
Green Ash FS-5, pre-EABFS-5_23Illumina MiSeq703,923194,181,616
Green Ash FS-4, post-EAB (8 weeks after egg application)FS-4 egg_22Illumina MiSeq658,593181,574,854
Green Ash FS-3, pre-EABFS-3_21Illumina MiSeq759,934207,962,455
Green Ash FS-2, post-EAB (8 weeks after egg application)FS-2 egg_20Illumina MiSeq615,545169,384,558
Green Ash petiole mechanical wounding-24hrGA-WP_19Illumina MiSeq642,762180,648,181
Green Ash petiole mechanical wounding-5hrGA-WP-1_18Illumina MiSeq626,118176,386,151
Green Ash leaf mechanical wounding-24hrGA-WL_17Illumina MiSeq720,794200,661,296
Green Ash leaf mechanical wounding-5hrGA-WL-1_16Illumina MiSeq725,951201,900,631
Green Ash Root-controlGA-COR_15Illumina MiSeq699,454190,329,305
Green Ash Petiole-controlGA-COP_14Illumina MiSeq770,075209,399,722
Green Ash ozone 12 - 28 days, 225ppbGA-CH12-28D_12Illumina MiSeq159,44448,152,088
Green Ash ozone 11 - 28 days, 125ppbGA-CH11-28D_11Illumina MiSeq258,32278,013,244
Green Ash ozone 10 - 28 days, 80ppbGA-CH10-28D_10Illumina MiSeq243,47573,529,450
Green Ash ozone 9 - 28 days, controlGA-CH9-28D_9Illumina MiSeq220,43266,570,464
Green Ash ozone 8 - 14 days, 225ppbGA-CH12-14D_8Illumina MiSeq241,87173,045,042
Green Ash ozone 7 - 14 days, 125ppbGA-CH11-14D_7Illumina MiSeq253,81776,652,734
Green Ash ozone 6 - 14 days, 80ppbGA-CH10-14D_6Illumina MiSeq213,64964,521,998
Green Ash ozone 5 - 14 days, controlGA-CH9-14D_5Illumina MiSeq225,46668,090,732
Green Ash ozone 4 - 7 hrs, 225ppbGA-CH12-7hr_4Illumina MiSeq250,05975,517,818
Green Ash ozone 3 - 7 hrs, 125ppbGA-CH11-7hr_3Illumina MiSeq247,86474,854,928
Green Ash ozone 2 - 7 hrs, 80ppbGA-CH10-7hr_2Illumina MiSeq228,55969,024,818
Green Ash ozone 1 - 7 hrs, controlGA-CH9-7hr_1Illumina MiSeq209,53263,278,664
TOTAL29,932,5038,455,943,291

Illumina HiSeq 2000 Data

Scroll up forMiSeq Data
Library DescriptionLibrary CodePlatformHiSeq ReadsHiSeq Bases
Green Ash Leaf-controlGA-COL_54Illumina HiSeq 200011,797,2352,383,041,470
Green ash control chamber ozone 10ppbGA OW-9_96Illumina HiSeq 20005,009,9171,012,003,234
Green ash ozone exposure 225ppb for 29 day + mecanical wounding on day 28GA OW-12_95Illumina HiSeq 20005,900,8711,191,975,942
Green ash ozone exposure 125ppb for 29 day + mecanical wounding on day 28GA OW-11_94Illumina HiSeq 20005,485,1321,107,996,664
Green ash ozone exposure 80ppb for 29 day + mecanical wounding on day 28GA OW-10_93Illumina HiSeq 20006,235,8631,259,644,326
Green ash root heat (40C) exposure for 24hrGA-HR_92Illumina HiSeq 20006,328,1601,278,288,320
Green ash petiole heat (40C) exposure for 24hrGA-HP_91Illumina HiSeq 20006,141,7141,240,626,228
Green ash leaf heat (40C) exposure for 24hrGA-HL_90Illumina HiSeq 20006,684,4001,350,248,800
Green ash root drought(<1.0 mpa)GA-DR_89Illumina HiSeq 20008,870,2331,791,787,066
Green ash petiole drought(<1.0 mpa)GA-DP_88Illumina HiSeq 20009,537,1191,926,498,038
Green ash leaf drought(<1.0 mpa)GA-DL_87Illumina HiSeq 20007,331,2291,480,908,258
Green Ash root cold (4C) 0 time point controlGA-CR_86Illumina HiSeq 20008,859,8171,789,683,034
Green Ash petiole cold (4C) 0 time point controlGA-CP_85Illumina HiSeq 20008,808,1941,779,255,188
Green Ash leaf cold (4C) 0 time point controlGA-CL_84Illumina HiSeq 20007,326,8021,480,014,004
Green Ash root cold (4C) exposure for 24hr24-GA-CR_83Illumina HiSeq 200010,332,9032,087,246,406
Green Ash petiole cold (4C) exposure for 24hr24-GA-CP_82Illumina HiSeq 20007,148,8301,444,063,660
Green Ash leaf cold (4C) exposure for24hr24-GA-CL_81Illumina HiSeq 200012,878,5692,601,470,938
Green Ash terminal budsGA M-8_80Illumina HiSeq 20006,882,0651,390,177,130
Green Ash axial budsGA M-7_79Illumina HiSeq 20006,317,9161,276,219,032
Green Ash seed wingsGA M-6_78Illumina HiSeq 200016,244,5043,281,389,808
Green Ash damaged twigs-1 year oldGA M-4_76Illumina HiSeq 20006,622,4831,337,741,566
Green Ash undamaged twigs-1 year oldGA M-3_75Illumina HiSeq 20005,436,4691,098,166,738
Green Ash damaged leaflets-hole punchedGA M-2_74Illumina HiSeq 20006,612,6181,335,748,836
Green Ash undamaged leafletsGA M-1_73Illumina HiSeq 20005,053,4861,020,804,172
Green Ash FS-12, post-EAB (8 weeks after egg application)FS-12 egg_72Illumina HiSeq 200015,247,2583,079,946,116
Green Ash FS-11, pre-EABFS-11_71Illumina HiSeq 200029,548,6115,968,819,422
Green Ash FS-10, post-EAB (8 weeks after egg application)FS-10 egg_70Illumina HiSeq 200012,392,0122,503,186,424
Green Ash FS-9, pre-EABFS-9_69Illumina HiSeq 200012,592,4162,543,668,032
Green Ash FS-8, post-EAB (8 weeks after egg application)FS-8 egg_68Illumina HiSeq 200012,736,1322,572,698,664
Green Ash 3 year old tissue for xilemGA M-5_77Illumina HiSeq 20001,702,550343,915,100
Green Ash FS-7, pre-EABFS-7_67Illumina HiSeq 200012,390,1912,502,818,582
Green Ash FS-6, post-EAB (8 weeks after egg application)FS-6 egg_66Illumina HiSeq 200010,149,1962,050,137,592
Green Ash FS-5, pre-EABFS-5_65Illumina HiSeq 200013,841,1892,795,920,178
Green Ash FS-4, post-EAB (8 weeks after egg application)FS-4 egg_64Illumina HiSeq 200013,134,0952,653,087,190
Green Ash FS-3, pre-EABFS-3_63Illumina HiSeq 200011,748,5082,373,198,616
Green Ash FS-2, post-EAB (8 weeks after egg application)FS-2 egg_62Illumina HiSeq 200011,198,4922,262,095,384
Green Ash FS-1, pre-EABFS-1_61Illumina HiSeq 200026,005,5935,253,129,786
Green Ash petiole mechanical wounding-24hrGA-WP_60Illumina HiSeq 200012,191,9872,462,781,374
Green Ash petiole mechanical wounding-5hrGA-WP-1_59Illumina HiSeq 200011,030,1282,228,085,856
Green Ash leaf mechanical wounding-24hrGA-WL_58Illumina HiSeq 200013,228,9862,672,255,172
Green Ash leaf mechanical wounding-5hrGA-WL-1_57Illumina HiSeq 200011,583,8172,339,931,034
Green Ash Root-controlGA-COR_56Illumina HiSeq 200013,989,7062,825,920,612
Green Ash Petiole-controlGA-COP_55Illumina HiSeq 200014,345,0572,897,701,514
TOTAL446,902,45390,274,295,506
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