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Title: Defining the maize transcriptome de novo using deep RNA-Seq

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.
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Conference: 6th Annual DOE JGI User Meeting , Walnut Creek, CA, 3/22 - 3/24/2011
Research Org:
Ernest Orlando Lawrence Berkeley National Laboratory, Berkeley, CA (US)
Sponsoring Org:
Genomics Division
Country of Publication:
United States
99; 97 de novo assembly, RNA-sequencing, informatics, eukaryotes, transcript variants, gene annotations