Overview
Analysis Namede novo Green ash (Fraxinus pennsylvanica)
Transcriptome NameFraxinus pennsylvanica 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 Contigs107,611
OrganismsFraxinus pennsylvanica

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 107,611
Transcript N50 1,327 bp
Transcript Average Length 818 bp
Number of Proteins 52,899
Protein N50 352 aa
Protein Average Length 285 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 Description Library Code Platform MiSeq Reads MiSeq Bases
Green Ash Leaf-control GA-COL_13 Illumina MiSeq 679,517 184,481,554
Green ash control chamber ozone 10ppb GA OW-9_53 Illumina MiSeq 352,040 100,212,219
Green ash ozone exposure 225ppb for 29 day + mecanical wounding on day 28 GA OW-12_52 Illumina MiSeq 352,289 100,081,024
Green ash ozone exposure 125ppb for 29 day + mecanical wounding on day 28 GA OW-11_51 Illumina MiSeq 306,848 87,140,122
Green ash ozone exposure 80ppb for 29 day + mecanical wounding on day 28 GA OW-10_50 Illumina MiSeq 344,500 97,989,386
Green ash root heat (40C) exposure for 24hr GA-HR_49 Illumina MiSeq 379,593 108,085,633
Green ash petiole heat (40C) exposure for 24hr GA-HP_48 Illumina MiSeq 383,170 108,952,578
Green ash leaf heat (40C) exposure for 24hr GA-HL_47 Illumina MiSeq 399,220 113,997,045
Green ash root drought( GA-DR_46 Illumina MiSeq 562,139 160,480,214
Green ash petiole drought( GA-DP_45 Illumina MiSeq 584,023 167,177,488
Green ash leaf drought( GA-DL_44 Illumina MiSeq 660,912 188,252,692
Green Ash root cold (4C) 0 time point control GA-CR_43 Illumina MiSeq 575,597 163,144,120
Green Ash petiole cold (4C) 0 time point control GA-CP_42 Illumina MiSeq 531,475 151,227,565
Green Ash leaf cold (4C) 0 time point control GA-CL_41 Illumina MiSeq 485,738 137,925,562
Green Ash root cold (4C) exposure for 24hr 24-GA-CR_40 Illumina MiSeq 512,688 146,651,958
Green Ash petiole cold (4C) exposure for 24hr 24-GA-CP_39 Illumina MiSeq 438,573 125,271,028
Green Ash leaf cold (4C) exposure for24hr 24-GA-CL_38 Illumina MiSeq 1,802,378 510,732,344
Green Ash terminal buds GA M-8_37 Illumina MiSeq 383,853 109,745,634
Green Ash axial buds GA M-7_36 Illumina MiSeq 388,060 110,648,513
Green Ash seed wings GA M-6_35 Illumina MiSeq 2,016,332 576,094,593
Green Ash 3 year old tissue for xilem GA M-5_34 Illumina MiSeq 2,393,054 674,340,974
Green Ash damaged twigs-1 year old GA M-4_33 Illumina MiSeq 456,291 130,748,682
Green Ash undamaged twigs-1 year old GA M-3_32 Illumina MiSeq 325,611 92,780,707
Green Ash damaged leaflets-hole punched GA M-2_31 Illumina MiSeq 428,915 121,834,598
Green Ash undamaged leaflets GA M-1_30 Illumina MiSeq 361,217 102,968,873
Green Ash FS-12, post-EAB (8 weeks after egg application) FS-12 egg_29 Illumina MiSeq 779,414 215,297,514
Green Ash FS-10, post-EAB (8 weeks after egg application) FS-10 egg_28 Illumina MiSeq 779,311 210,302,624
Green Ash FS-9, pre-EAB FS-9_27 Illumina MiSeq 655,536 179,802,000
Green Ash FS-8, post-EAB (8 weeks after egg application) FS-8 egg_26 Illumina MiSeq 671,151 186,759,904
Green Ash FS-7, pre-EAB FS-7_25 Illumina MiSeq 631,463 174,071,104
Green Ash FS-6, post-EAB (8 weeks after egg application) FS-6 egg_24 Illumina MiSeq 635,956 175,064,290
Green Ash FS-5, pre-EAB FS-5_23 Illumina MiSeq 703,923 194,181,616
Green Ash FS-4, post-EAB (8 weeks after egg application) FS-4 egg_22 Illumina MiSeq 658,593 181,574,854
Green Ash FS-3, pre-EAB FS-3_21 Illumina MiSeq 759,934 207,962,455
Green Ash FS-2, post-EAB (8 weeks after egg application) FS-2 egg_20 Illumina MiSeq 615,545 169,384,558
Green Ash petiole mechanical wounding-24hr GA-WP_19 Illumina MiSeq 642,762 180,648,181
Green Ash petiole mechanical wounding-5hr GA-WP-1_18 Illumina MiSeq 626,118 176,386,151
Green Ash leaf mechanical wounding-24hr GA-WL_17 Illumina MiSeq 720,794 200,661,296
Green Ash leaf mechanical wounding-5hr GA-WL-1_16 Illumina MiSeq 725,951 201,900,631
Green Ash Root-control GA-COR_15 Illumina MiSeq 699,454 190,329,305
Green Ash Petiole-control GA-COP_14 Illumina MiSeq 770,075 209,399,722
Green Ash ozone 12 - 28 days, 225ppb GA-CH12-28D_12 Illumina MiSeq 159,444 48,152,088
Green Ash ozone 11 - 28 days, 125ppb GA-CH11-28D_11 Illumina MiSeq 258,322 78,013,244
Green Ash ozone 10 - 28 days, 80ppb GA-CH10-28D_10 Illumina MiSeq 243,475 73,529,450
Green Ash ozone 9 - 28 days, control GA-CH9-28D_9 Illumina MiSeq 220,432 66,570,464
Green Ash ozone 8 - 14 days, 225ppb GA-CH12-14D_8 Illumina MiSeq 241,871 73,045,042
Green Ash ozone 7 - 14 days, 125ppb GA-CH11-14D_7 Illumina MiSeq 253,817 76,652,734
Green Ash ozone 6 - 14 days, 80ppb GA-CH10-14D_6 Illumina MiSeq 213,649 64,521,998
Green Ash ozone 5 - 14 days, control GA-CH9-14D_5 Illumina MiSeq 225,466 68,090,732
Green Ash ozone 4 - 7 hrs, 225ppb GA-CH12-7hr_4 Illumina MiSeq 250,059 75,517,818
Green Ash ozone 3 - 7 hrs, 125ppb GA-CH11-7hr_3 Illumina MiSeq 247,864 74,854,928
Green Ash ozone 2 - 7 hrs, 80ppb GA-CH10-7hr_2 Illumina MiSeq 228,559 69,024,818
Green Ash ozone 1 - 7 hrs, control GA-CH9-7hr_1 Illumina MiSeq 209,532 63,278,664
TOTAL 29,932,503 8,455,943,291



Illumina HiSeq 2000 Data

Scroll up forMiSeq Data

Library Description Library Code Platform HiSeq Reads HiSeq Bases
Green Ash Leaf-control GA-COL_54 Illumina HiSeq 2000 11,797,235 2,383,041,470
Green ash control chamber ozone 10ppb GA OW-9_96 Illumina HiSeq 2000 5,009,917 1,012,003,234
Green ash ozone exposure 225ppb for 29 day + mecanical wounding on day 28 GA OW-12_95 Illumina HiSeq 2000 5,900,871 1,191,975,942
Green ash ozone exposure 125ppb for 29 day + mecanical wounding on day 28 GA OW-11_94 Illumina HiSeq 2000 5,485,132 1,107,996,664
Green ash ozone exposure 80ppb for 29 day + mecanical wounding on day 28 GA OW-10_93 Illumina HiSeq 2000 6,235,863 1,259,644,326
Green ash root heat (40C) exposure for 24hr GA-HR_92 Illumina HiSeq 2000 6,328,160 1,278,288,320
Green ash petiole heat (40C) exposure for 24hr GA-HP_91 Illumina HiSeq 2000 6,141,714 1,240,626,228
Green ash leaf heat (40C) exposure for 24hr GA-HL_90 Illumina HiSeq 2000 6,684,400 1,350,248,800
Green ash root drought( GA-DR_89 Illumina HiSeq 2000 8,870,233 1,791,787,066
Green ash petiole drought( GA-DP_88 Illumina HiSeq 2000 9,537,119 1,926,498,038
Green ash leaf drought( GA-DL_87 Illumina HiSeq 2000 7,331,229 1,480,908,258
Green Ash root cold (4C) 0 time point control GA-CR_86 Illumina HiSeq 2000 8,859,817 1,789,683,034
Green Ash petiole cold (4C) 0 time point control GA-CP_85 Illumina HiSeq 2000 8,808,194 1,779,255,188
Green Ash leaf cold (4C) 0 time point control GA-CL_84 Illumina HiSeq 2000 7,326,802 1,480,014,004
Green Ash root cold (4C) exposure for 24hr 24-GA-CR_83 Illumina HiSeq 2000 10,332,903 2,087,246,406
Green Ash petiole cold (4C) exposure for 24hr 24-GA-CP_82 Illumina HiSeq 2000 7,148,830 1,444,063,660
Green Ash leaf cold (4C) exposure for24hr 24-GA-CL_81 Illumina HiSeq 2000 12,878,569 2,601,470,938
Green Ash terminal buds GA M-8_80 Illumina HiSeq 2000 6,882,065 1,390,177,130
Green Ash axial buds GA M-7_79 Illumina HiSeq 2000 6,317,916 1,276,219,032
Green Ash seed wings GA M-6_78 Illumina HiSeq 2000 16,244,504 3,281,389,808
Green Ash damaged twigs-1 year old GA M-4_76 Illumina HiSeq 2000 6,622,483 1,337,741,566
Green Ash undamaged twigs-1 year old GA M-3_75 Illumina HiSeq 2000 5,436,469 1,098,166,738
Green Ash damaged leaflets-hole punched GA M-2_74 Illumina HiSeq 2000 6,612,618 1,335,748,836
Green Ash undamaged leaflets GA M-1_73 Illumina HiSeq 2000 5,053,486 1,020,804,172
Green Ash FS-12, post-EAB (8 weeks after egg application) FS-12 egg_72 Illumina HiSeq 2000 15,247,258 3,079,946,116
Green Ash FS-11, pre-EAB FS-11_71 Illumina HiSeq 2000 29,548,611 5,968,819,422
Green Ash FS-10, post-EAB (8 weeks after egg application) FS-10 egg_70 Illumina HiSeq 2000 12,392,012 2,503,186,424
Green Ash FS-9, pre-EAB FS-9_69 Illumina HiSeq 2000 12,592,416 2,543,668,032
Green Ash FS-8, post-EAB (8 weeks after egg application) FS-8 egg_68 Illumina HiSeq 2000 12,736,132 2,572,698,664
Green Ash 3 year old tissue for xilem GA M-5_77 Illumina HiSeq 2000 1,702,550 343,915,100
Green Ash FS-7, pre-EAB FS-7_67 Illumina HiSeq 2000 12,390,191 2,502,818,582
Green Ash FS-6, post-EAB (8 weeks after egg application) FS-6 egg_66 Illumina HiSeq 2000 10,149,196 2,050,137,592
Green Ash FS-5, pre-EAB FS-5_65 Illumina HiSeq 2000 13,841,189 2,795,920,178
Green Ash FS-4, post-EAB (8 weeks after egg application) FS-4 egg_64 Illumina HiSeq 2000 13,134,095 2,653,087,190
Green Ash FS-3, pre-EAB FS-3_63 Illumina HiSeq 2000 11,748,508 2,373,198,616
Green Ash FS-2, post-EAB (8 weeks after egg application) FS-2 egg_62 Illumina HiSeq 2000 11,198,492 2,262,095,384
Green Ash FS-1, pre-EAB FS-1_61 Illumina HiSeq 2000 26,005,593 5,253,129,786
Green Ash petiole mechanical wounding-24hr GA-WP_60 Illumina HiSeq 2000 12,191,987 2,462,781,374
Green Ash petiole mechanical wounding-5hr GA-WP-1_59 Illumina HiSeq 2000 11,030,128 2,228,085,856
Green Ash leaf mechanical wounding-24hr GA-WL_58 Illumina HiSeq 2000 13,228,986 2,672,255,172
Green Ash leaf mechanical wounding-5hr GA-WL-1_57 Illumina HiSeq 2000 11,583,817 2,339,931,034
Green Ash Root-control GA-COR_56 Illumina HiSeq 2000 13,989,706 2,825,920,612
Green Ash Petiole-control GA-COP_55 Illumina HiSeq 2000 14,345,057 2,897,701,514
TOTAL 446,902,453 90,274,295,506