Barley Expression Database
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Project Summary

Barley is one of the world's most important cereal crops used for food, malt and animal feed. However it has a relatively large genome size (5 Gbp) which inhibits full-scale analysis of the genome structure by sequencing. An alternative way to understanding the structure and function of the barley genes is by full-length cDNA approach. From 2005, the cDNA libraries of malting barley ( Hordeum vulgare cv. Haruna Nijo) using the "cap-trapper" method have been constructed as part of the Green-Techno Program led by Japanese MAFF.
The conditions for preparation of RNA materials for cDNA construction are as follows. Each cDNA sequence is identified for its origin of tissue by the 8-base sequence tag identifier listed below.

Library Tag No. Tissue Brevity code Tag sequence Tag comlement
N library 1-1 Flag leaf FGL TACGTACG CGTACGTA
1-2 Cold treatment shoot CTS CATGTACG CGTACATG
1-3 Haruna normal shoot
(Shaded or water culture)
HNS CTGATACG CGTATCAG
1-4 Germinated shoot GST GTCATACG CGTATGAC
S library 2-1 Hydroponic aluminium treated plant HAP CTGACATG CATGTCAG
2-2 Hydroponic drought stress or salt stress HDS TACGCATG CATGCGTA
2-3 ABA treatment plant ABP GTCACATG CATGTGAC
2-4 JA treatment plant JAP CTGACTGA TCAGTCAG
PMF library 3-1 Young spike panicle YSP TACGCTGA TCAGCGTA
3-2 Flower in heading FLH CATGCTGA TCAGCATG
3-3 Flower in maturing FLM GTCACTGA TCAGTGAC
3-4 Germinated seed GMS GTCAGTCA TGACTGAC

After construction of library, 96 clones of each library were picked randomly and measure the length of insert DNA to verify quality of these libraries. cDNA clones were cut by PvuII and load in 1.5% agarose gel with 500 bp ladder marker. The insert lengths of 3 pooled libraries were 1.5-1.7 kb and all three libraries were considered reasonable as the length of plant full length cDNA library. 172,800 clones (57,600 sequences for each library) were sequenced both end with BDT v3.1 and ABI3700 and check read length with Phred. The read length in this study was more than 500 bp and considered reasonable. 567 clones of representative clones had homolog of TEs or chloroplast, so these clones were removed from list of full-length sequencing. The 3' end sequences were clustered independently based on BLAST analysis of end sequences and clones with the most 5' proximal sequences in each group are selected as representative clones and being used for full-length sequencing with primer-walking. In this database, all the 5' and 3' end sequences from the libraries are used for sequence clustering, and the resulted contigs are presented for further investigation.