skip to main content
OSTI.GOV title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: JGI Plant Genomics Gene Annotation Pipeline

Abstract

Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

Authors:
; ; ; ;
Publication Date:
Research Org.:
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Sponsoring Org.:
Genomics Division
OSTI Identifier:
1241222
Report Number(s):
LBNL-7040E
DOE Contract Number:  
DE-AC02-05CH11231
Resource Type:
Conference
Resource Relation:
Conference: American Society of Plant Biologists, Portland, Oregon, 2014
Country of Publication:
United States
Language:
English
Subject:
99 GENERAL AND MISCELLANEOUS

Citation Formats

Shu, Shengqiang, Rokhsar, Dan, Goodstein, David, Hayes, David, and Mitros, Therese. JGI Plant Genomics Gene Annotation Pipeline. United States: N. p., 2014. Web.
Shu, Shengqiang, Rokhsar, Dan, Goodstein, David, Hayes, David, & Mitros, Therese. JGI Plant Genomics Gene Annotation Pipeline. United States.
Shu, Shengqiang, Rokhsar, Dan, Goodstein, David, Hayes, David, and Mitros, Therese. Mon . "JGI Plant Genomics Gene Annotation Pipeline". United States. doi:. https://www.osti.gov/servlets/purl/1241222.
@article{osti_1241222,
title = {JGI Plant Genomics Gene Annotation Pipeline},
author = {Shu, Shengqiang and Rokhsar, Dan and Goodstein, David and Hayes, David and Mitros, Therese},
abstractNote = {Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Mon Jul 14 00:00:00 EDT 2014},
month = {Mon Jul 14 00:00:00 EDT 2014}
}

Conference:
Other availability
Please see Document Availability for additional information on obtaining the full-text document. Library patrons may search WorldCat to identify libraries that hold this conference proceeding.

Save / Share: