Large-Scale Collection and Analysis of Full-Length cDNAs from <i>Brachypodium distachyon</i> and Integration with Pooideae Sequence Resources

<div><p>A comprehensive collection of full-length cDNAs is essential for correct structural gene annotation and functional analyses of genes. We constructed a mixed full-length cDNA library from 21 different tissues of <i>Brachypodium distachyon</i> Bd21, and obtained 78,163 high quality expressed sequence tags (ESTs) from both ends of ca. 40,000 clones (including 16,079 contigs). We updated gene structure annotations of <i>Brachypodium</i> genes based on full-length cDNA sequences in comparison with the latest publicly available annotations. About 10,000 non-redundant gene models were supported by full-length cDNAs; ca. 6,000 showed some transcription unit modifications. We also found ca. 580 novel gene models, including 362 newly identified in Bd21. Using the updated transcription start sites, we searched a total of 580 plant <i>cis</i>-motifs in the −3 kb promoter regions and determined a genome-wide <i>Brachypodium</i> promoter architecture. Furthermore, we integrated the <i>Brachypodium</i> full-length cDNAs and updated gene structures with available sequence resources in wheat and barley in a web-accessible database, the RIKEN <i>Brachypodium</i> FL cDNA database. The database represents a “one-stop” information resource for all genomic information in the Pooideae, facilitating functional analysis of genes in this model grass plant and seamless knowledge transfer to the Triticeae crops.</p>