Header

UZH-Logo

Maintenance Infos

Gene and repetitive sequence annotation in the Triticeae


Wicker, T; Buell, C R (2009). Gene and repetitive sequence annotation in the Triticeae. In: Feuillet, C; Muehlbauer, G J. Genetics and Genomics of the Triticeae. New York, US: Springer, 407-426.

Abstract

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes.

Abstract

The Triticeae tribe contains some of the world’s most important agricultural crops (wheat, barley and rye) and is perhaps, one of the most challenging for genome annotation because Triticeae genomes are primarily composed of repetitive sequences. Further complicating the challenge is the polyploidy found in wheat and particularly in the hexaploid bread wheat genome. Genomic sequence data are available for the Triticeae in the form of large collections of Expressed Sequence Tags (>1.5 million) and an increasing number of bacterial artificial chromosome clone sequences. Given that high repetitive sequence content in the Triticeae confounds annotation of protein-coding genes, repetitive sequences have been identified, annotated, and collated into public databases. Protein coding genes in the Triticeae are structurally annotated using a combination of ab initio gene finders and experimental evidence. Functional annotation of protein coding genes involves assessment of sequence similarity to known proteins, expression evidence, and the presence of domain and motifs. Annotation methods and tools for Triticeae genomic sequences have been adapted from existing plant genome annotation projects and were designed to allow for flexibility of single sequence annotation while allowing a whole community annotation effort to be developed. With the availability of an increasing number of annotated grass genomes, comparative genomics can be exploited to accelerate and enhance the quality of Triticeae sequences annotation. This chapter provides a brief overview of the Triticeae genomes features that are challenging for genome annotation and describes the resources and methods available for sequence annotation with a particular emphasis on problems caused by the repetitive fraction of these genomes.

Statistics

Citations

Dimensions.ai Metrics

Altmetrics

Downloads

203 downloads since deposited on 16 Feb 2010
29 downloads since 12 months
Detailed statistics

Additional indexing

Item Type:Book Section, refereed, original work
Communities & Collections:07 Faculty of Science > Department of Plant and Microbial Biology
Dewey Decimal Classification:580 Plants (Botany)
Language:English
Date:2009
Deposited On:16 Feb 2010 08:52
Last Modified:18 Feb 2018 00:09
Publisher:Springer
Series Name:Plant Genetics and Genomics: Crops and Models
Number:7
ISBN:978-0-387-77488-6 (P) 978-0-387-77489-3 (E)
Additional Information:The original publication is available at www.springerlink.com
OA Status:Green
Publisher DOI:https://doi.org/10.1007/978-0-387-77489-3_15

Download

Download PDF  'Gene and repetitive sequence annotation in the Triticeae'.
Preview
Content: Accepted Version
Filetype: PDF
Size: 1MB
View at publisher