Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea (Eutrema salsugineum)

Table 1 Summary of T. salsuginea ESTs generated from 454 sequencing and assembled contigs

Library	Non-normalized	Normalized	Combined¹
Number of reads	811,683	400,631	1,212,314
Number of contaminated reads²	4,496	2,506	7,002
Average read length (bp)	566	257	464
Total reads (Mbp)	459.54	103.13	562.67
Number of assembled reads	712,262	376,509	1,060,666
Number of contigs³	33,870	28,928	46,220
Number of contigs with only 454 reads⁴	21,662	16,949	33,147
Average coverage	11.99	6.74	12.63
N50 (bp)	665	632	646
Average contig length (bp)	621	502	567
Number of contigs with ORF⁵	33,625	28,416	45,583
Number of Arabidopsis peptides found⁶	23,787	23,220	24,457

¹Combined 454 reads derived from normalized and non-normalized library.
²Best hits with E-value < 1e-10, non streptophyta sequences (NCBI, nr, nt, as of February 12, 2010).
³Includes publicly available T. salsuginea ESTs (as of April 19, 2010).
⁴Number of contigs minus number of contigs assembled with at least one publicly available EST.
⁵Open reading frames (ORFs) predicted including partial ORFs (Min et al. [83]).
⁶Any hits with E-value < 0.001 from BLASTX search against TAIR9 database (27,379 peptides).

ISSN: 1471-2164