Takashi Matsumoto¹, Tsuyoshi Tanaka², Hiroaki Sakai², Hiroyuki Kanamori¹, Kanako Kurita³, Kiyosumi Hori⁴, Takeshi Itoh², Kazuhiro Sato⁵

¹Plant Genome Research Unit, NIAS, ²Bioinformatics Research Unit, NIAS, ³Advanced Genomics Laboratory, NIAS, ⁴Rice Applied Genomics Research Unit, NIAS, ⁵Okayama University

［Abstract］

Full-length cDNA libraries of barley, whose complete genome is yet undetermined, were created and 24,783 representative cDNAs were fully sequenced. The information about these cDNAs and their functions was released from our database.

［Keywords］

barley, full-length cDNA, database

［Background］

The amount of barley production in the world is fourth largest. Barley is widely used as a food crop, a feed grain and raw material for beer. Several breeding projects to improve useful traits, such as disease resistance and vivipary, are currently underway. However, since the complete barley genome sequence is yet undetermined, large-scale studies have not been expedited so far. In this study, we aimed to collect from a barley cultivar a large amount of full-length cDNAs that reflect the functional forms of genes. Sequencing of the cDNAs will help provide comprehensive understanding of the barley genes and should ultimately lead to elucidation of the function of individual genes and agronomically important phenomena.

［Results and Discussion］

1. RNAs were extracted from a barley cultivar, Haruna Nijo, which was grown under several conditions, such as cold and dry stresses and exposure to hormones. We obtained ~172,000 clones of full-length cDNAs (FLcDNAs). After removal of redundant sequences, 24,783 were selected as representatives and were sequenced (Fig. 1). Of these FLcDNAs, 85% were inferred to contain complete protein-coding regions. Comparisons with the sequences in the RefSeq and UniProtKB databases resulted in predictions of 85% of the gene functions.
2. The barley sequences obtained in this study were compared to publicly available sequences of three cultivated species (rice, maize, sorghum) and one wild relative (Brachypodium). As a result, it was found that the four cultivated species share 87% of the genes. This observation indicates that the grass species sequences are highly conserved. Nonetheless, 1,699 barley genes did not show any homology to the known genes of the other grasses, so these genes might be related to characteristics specific to barley.
3. The FLcDNAs deciphered in this study are available in the public DNA database, DDBJ. In addition, the annotation and expression data were released from our barley full-length cDNA database (http://barleyflc.dna.affrc.go.jp/hvdb/index.html) on March 17th, 2011.

1. This study presented a comprehensive set of expressed functional genes of barley. It is expected that comparisons with genomes and genes of other species will accelerate studies of individual gene functions and development of molecular markers, so that the sequence information will be used for breeding of barley in the future.
2. In general, FLcDNAs contain the complete protein-coding regions. Transformation by introgression of FLcDNAs will help investigations of individual gene functions.
3. International collaborations of barley and wheat genome-wide sequencing efforts are currently underway. The barley FLcDNAs presented in this study will be vital for genome annotations of barley and wheat.

Fig. 1. Sequencing and data release of barley FLcDNAs RNAs were extracted from barley specimens, cDNAs were synthesized and full-length cDNAs were selected and cloned. Redundant sequences were discarded and 24,783 representatives were selected and sequenced. The sequences were released from our database.

[Reference]

1. Matsumoto T, Tanaka T, Sakai H, Amano N, Kanamori H, Kurita K, Kikuta A, Kamiya K, Yamamoto M, Ikawa H, Fujii N, Hori K, Itoh T, Sato K (2011) Comprehensive sequence analysis of 24,783 barley full-length cDNAs derived from 12 clone libraries Plant Physiology 156(1):20-28
2. Mayer K.F.X, Martis M, Hedley P.E, Šimková H, Liu H, Morris J.A, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Doležel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics The Plant Cell 23(4):1249-1263