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Table 1 Summary of wild barley 454 transcriptome sequencing, de novo assembly and annotation

From: Transcriptome sequencing of two wild barley (Hordeum spontaneum L.) ecotypes differentially adapted to drought stress reveals ecotype-specific transcripts

Analysis

B1K2

B1K30

B1K

Reads:

   

 No. of raw reads (Mbp)

575,918 (223.40)

562,862 (193.91)

1,138,780 (417.31)

 No. of reads after trimming (Mbp)

559,019 (199.22)

549,791 (171.81)

1,097,384 (370.75)

 Mean trimmed reads length (bp)

356

313

338

 Range of trimmed reads (bp)

20 – 1,080

20 – 1,009

20 – 1,080

 No. of aligned reads (Mbp)

529,779 (191.06)

522,279 (164.34)

1,054,990 (356.35)

De novo assembly:

   

 1No. of assembled reads (%)

529,297 (95)

522,093 (95)

1,035,947 (94)

 2No. of isotigs (Mbp)

15,956

16,711

23,675

 N50 (bp)

915

914

910

 No of singletons

6,235

6,618

9,383

Unigenes (≥100 bp):

   

 3All

20,503

21,553

28,828

 4Clustered

20,439

21,494

28,720

 Mean size (bp)

619

562

609

 Size (Mbp)

12.658

12.090

17.491

 ≥ 500 bp (%)

9,732 (63)

8,633 (54)

12,785 (59)

 ≥ 1000 bp (%)

3,044 (20)

2,621 (16)

4,609 (21)

Annotation: number (%) of annotated transcripts

 InterPro

4,300 (21)

5,137 (24)

7,153 (25)

 Pfam

3,829 (19)

4,469 (21)

6,335 (22)

 NR

13,637 (67)

13,532 (63)

5na

 Swiss-Prot

8,143 (40)

7,906 (37)

na

 GO

7,293 (36)

7,069 (33)

na

 KGG

6,612 (32)

6,102 (28)

na

  1. 1assembled reads: fully and partially assembled; 2isotigs: groups of contigs and large contigs; 3all: clustered isotigs + singletons; and 4clustered: clustered isotigs + true-singletons (putative unique transcripts, PUTs). 5na: analysis not performed.