Fraxinus pennsylvanica - Transcriptome Assembly

Summary

Name	Fraxinus pennsylvanica - Transcriptome Assembly
Resource Type	Transcriptome Assembly
Organism	F. pennsylvanica (Green Ash)
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	NCBI BioProject:273266

Publication

Lane T, Best T, Zembower N, Davitt J, Henry N, Xu Y, Koch J, Liang H, McGraw J, Schuster S, Shim D. The green ash transcriptome and identification of genes responding to abiotic and biotic stresses. BMC genomics. 2016 Dec;17(1):702.

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 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) Fraxinus_pennsylvanica_120313_transcripts.fasta
	Predicted ORFs (fasta format) Fraxinus_pennsylvanica_120313_peptides.fasta

Annotation

BLAST against the Swiss-prot protein database:

	Blastx, 1e-5 cutoff - 44% of transcripts matched a swiss-prot entry green_ash_sprot_nt.xlsx (Excel file with best hits)
	Blastp, 1e-5 cutoff - 72% of proteins matched a swiss-prot entry green_ash_sprot_aa.xlsx (Excel file with best hits)

BLAST against the Trembl protein database, only plant entries:

	Blastx, 1e-4 cutoff - 63% of transcripts matched a trembl entry green_ash_blastx_trembl.xlsx (Excel file with best hits)
	Blastp, 1e-5 cutoff - 95% of proteins matched a trembl entry green_ash_trembl_aa.xlsx (Excel file with best hits)

HMMER search against Pfam database

	Excel output of all hits Fraxinus_pennsylvanica_120313_proteins-pFam.xlsx
	Proteins assigned to GO terms inferred from pfam hits Fraxinus_pennsylvanica_120313_proteins-pFam-GOterms.xlsx

SSR Pipeline

	Excel file with statistics, SSR motifs and primers (484 high quality markers) Fraxinus_pennsylvanica_120313_transcripts.fasta.ssr_report.xlsx

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(<1.0 mpa)	GA-DR_46	Illumina MiSeq	562,139	160,480,214
Green ash petiole drought(<1.0 mpa)	GA-DP_45	Illumina MiSeq	584,023	167,177,488
Green ash leaf drought(<1.0 mpa)	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(<1.0 mpa)	GA-DR_89	Illumina HiSeq 2000	8,870,233	1,791,787,066
Green ash petiole drought(<1.0 mpa)	GA-DP_88	Illumina HiSeq 2000	9,537,119	1,926,498,038
Green ash leaf drought(<1.0 mpa)	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