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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.