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Title: 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}
}

Conference:
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