Tsuyoshi Tanaka¹, Takashi Matsumoto²

¹Bioinformatics Research Unit, ²Plant Genome Research Unit

［Abstract］

We used the sequence information of barley full-length cDNAs to determine the gene structures predicted in the genome thereby making significant contribution in the overall effort of characterizing 26,159 genes on the entire barley genome sequence. As a result, we were able to provide valuable information for accurate genome annotation, and detected genes of agronomic importance, which could be useful in barley breeding.

［Keywords］

barley, genome sequencing, full-length cDNA, annotation

［Background］

Barley is an important crop with an annual global production of about 130 million tons. The development of novel varieties with desirable traits such as high yield and tolerance to biotic/abiotic stresses is therefore highly anticipated as a solution to food shortage due to an ever-increasing population. Deciphering the genome sequence and characterization of gene structure and function will accelerate our understanding of its biology with implications in agriculture. The International Barley Sequencing Consortium (IBSC) released the estimated 5.1 Gbp barley genome assembly in 2012. As our contribution in elucidating the barley genome structure and function, we conducted an accurate annotation using the barley full-length cDNAs (FLcDNAs), and constructed a barley gene set in combination with other transcriptome data.

［Results and Discussion］

1. A total of 23,343 nonredundant barley transcripts were obtained from 28,621 FLcDNAs derived from a Japanese barley cultivar “Haruna Nijo” (Fig. 1).
2. These FLcDNAs were mapped onto the genome assembly generated by the IBSC based on a malting barley cultivar “Morex” using a gene prediction pipeline originally developed for rice. As a result, we were able to map and clarify the structures of 9,275 genes.
3. The structures of 79,379 expressed genes were determined in combination with the FLcDNA and the RNA-Seq data derived from the IBSC (Fig. 2). Moreover, by comparing the barley genes with gene sets of Brachypodium distachyon, rice, sorghum, and Arabidopsis, a barley gene set with 26,159 ‘high-confidence’ genes was identified.
4. We compared the genomic positions of orthologs between barley and B. distachyon, and clarified the evolutionary relationships, conservation of gene location, gene diversification, and gene functions.

1. An accurate information of genes predicted on the barley genome is expected to facilitate the isolation of useful genes and clarification of gene functions.
2. Breeding based on the genome information will accelerate the development of new cultivars with useful traits such as high-yield and disease resistance.
3. The barley genome sequence and gene annotation data will be indispensable in elucidating the wheat genome, which is 3x in size, as well as other Triticeae species.
4. Development of an informatics infrastructure with a genome browser to facilitate visualization of gene structure and function will enhance genomics-based breeding of barley.

Fig.1. Overview of gene annotation based on barley FLcDNAs.

Fig.2. Accurate analysis of barley genes using FLcDNAs.

 

[Reference]

1. The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome Nature 491(7426):711-716