Defining the maize transcriptome de novo using deep RNA-Seq [electronic resource]

• Ngôn ngữ: eng
• Ký hiệu phân loại: 668.5 Perfumes and cosmetics
• Thông tin xuất bản: Berkeley, Calif. : Oak Ridge, Tenn. : Lawrence Berkeley National Laboratory ; Distributed by the Office of Scientific and Technical Information, U.S. Dept. of Energy, 2011
• Mô tả vật lý: Size: 1 : , digital, PDF file.
• Bộ sưu tập: Metadata
• ID: 265471
• Chủ đề: 1. 09 biomass fuels; 2. 97 mathematical methods and computing; 3. 99 general and miscellaneousmathematics, computing, and information science; 4. Functionals; 5. Genes

Tóm tắt

De novo assembly of the transcriptome is crucial for functional genomics studies in bioenergy research, since many of the organisms lack high quality reference genomes. In a previous study we successfully de novo assembled simple eukaryote transcriptomes exclusively from short Illumina RNA-Seq reads [1]. However, extensive alternative splicing, present in most of the higher eukaryotes, poses a significant challenge for current short read assembly processes. Furthermore, the size of next-generation datasets, often large for plant genomes, presents an informatics challenge. To tackle these challenges we present a combined experimental and informatics strategy for de novo assembly in higher eukaryotes. Using maize as a test case, preliminary results suggest our approach can resolve transcript variants and improve gene annotations.