Defining the maize transcriptome de novo using deep RNA-Seq
Abstract
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.
- Authors:
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- Genomics Division
- OSTI Identifier:
- 1050662
- Report Number(s):
- LBNL-4782E-Poster-Pt1
- DOE Contract Number:
- DE-AC02-05CH11231
- Resource Type:
- Conference
- Resource Relation:
- Conference: 6th Annual DOE JGI User Meeting , Walnut Creek, CA, 3/22 - 3/24/2011
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 99; 97; de novo assembly, RNA-sequencing, informatics, eukaryotes, transcript variants, gene annotations
Citation Formats
Martin, Jeffrey, Gross, Stephen, Choi, Cindy, Zhang, Tao, Lindquist, Erika, Wei, Chia-Lin, and Wang, Zhong. Defining the maize transcriptome de novo using deep RNA-Seq. United States: N. p., 2011.
Web.
Martin, Jeffrey, Gross, Stephen, Choi, Cindy, Zhang, Tao, Lindquist, Erika, Wei, Chia-Lin, & Wang, Zhong. Defining the maize transcriptome de novo using deep RNA-Seq. United States.
Martin, Jeffrey, Gross, Stephen, Choi, Cindy, Zhang, Tao, Lindquist, Erika, Wei, Chia-Lin, and Wang, Zhong. 2011.
"Defining the maize transcriptome de novo using deep RNA-Seq". United States. https://www.osti.gov/servlets/purl/1050662.
@article{osti_1050662,
title = {Defining the maize transcriptome de novo using deep RNA-Seq},
author = {Martin, Jeffrey and Gross, Stephen and Choi, Cindy and Zhang, Tao and Lindquist, Erika and Wei, Chia-Lin and Wang, Zhong},
abstractNote = {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.},
doi = {},
url = {https://www.osti.gov/biblio/1050662},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Thu Jun 02 00:00:00 EDT 2011},
month = {Thu Jun 02 00:00:00 EDT 2011}
}