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Digital gene expression analysis of the hop (Humulus lupulus L.) transcriptome

Pitra, N., Schwekendiek, A., Matthews, P.
Acta horticulturae 2019 no.1236 pp. 135-144
Humulus lupulus, brewing industry, complementary DNA, cost effectiveness, data collection, gene expression, gene ontology, leaves, medicinal plants, messenger RNA, nucleotide sequences, specialty crops, transcriptome, trichomes
Humulus lupulus is a specialty crop with new-use potential beyond its most common application in the brewing industry. As a medicinal plant already used in the food industgry, hop is a compelling candidate for further scientific exploration, especially biochemical and molecular genetic studies. Yet because hop is a niche crop, crop improvement studies must have superior cost efficiency. Digital gene expression (DGE) is a low-cost method which allows for deep, quantitative gene transcript analysis. DGE analyses of three hop organs, cone, leaf and trichome glandular cells, yielded about 1.5 million cDNA sequence reads (tags) of 20 bp each in length which could not be assembled into large contigs. Therefore, a protocol to annotate the DGE tags was created, applied and compared to previously produced long-read transcriptomes. In order to organize and validate the transcript quantitations, the tagged, combined sequence dataset was grouped according to a gene ontology (GO) hierarchy. The combination of these sequencing technologies produced a well annotated, accurate, gene expression profile of the hop transcriptomes.