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.
- Research Organization:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Organization:
- Genomics Division
- DOE Contract Number:
- DE-AC02-05CH11231
- OSTI ID:
- 1050660
- Report Number(s):
- LBNL-4782E-Poster-Pt2; TRN: US201218%%872
- Resource Relation:
- Conference: Sequencing, Finishing and Analysis in the Future Meeting, Santa Fe, Mexico, 6/1 - 6/3/2011
- Country of Publication:
- United States
- Language:
- English
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