Applications and challenges of next-generation sequencing in Brassica species

Wei, Lijuan, Xiao, Meili, Hayward, Alice and Fu, Donghui (2013) Applications and challenges of next-generation sequencing in Brassica species. Planta, 238 6: 1005-1024. doi:10.1007/s00425-013-1961-6


Author Wei, Lijuan
Xiao, Meili
Hayward, Alice
Fu, Donghui
Title Applications and challenges of next-generation sequencing in Brassica species
Formatted title
Applications and challenges of next-generation sequencing in Brassica species
Journal name Planta   Check publisher's open access policy
ISSN 0032-0935
1432-2048
Publication date 2013-12-01
Year available 2013
Sub-type Critical review of research, literature review, critical commentary
DOI 10.1007/s00425-013-1961-6
Open Access Status Not Open Access
Volume 238
Issue 6
Start page 1005
End page 1024
Total pages 20
Place of publication Heidelberg, Germany
Publisher Springer
Language eng
Abstract Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.
Formatted abstract
Next-generation sequencing (NGS) produces numerous (often millions) short DNA sequence reads, typically varying between 25 and 400 bp in length, at a relatively low cost and in a short time. This revolutionary technology is being increasingly applied in whole-genome, transcriptome, epigenome and small RNA sequencing, molecular marker and gene discovery, comparative and evolutionary genomics, and association studies. The Brassica genus comprises some of the most agro-economically important crops, providing abundant vegetables, condiments, fodder, oil and medicinal products. Many Brassica species have undergone the process of polyploidization, which makes their genomes exceptionally complex and can create difficulties in genomics research. NGS injects new vigor into Brassica research, yet also faces specific challenges in the analysis of complex crop genomes and traits. In this article, we review the advantages and limitations of different NGS technologies and their applications and challenges, using Brassica as an advanced model system for agronomically important, polyploid crops. Specifically, we focus on the use of NGS for genome resequencing, transcriptome sequencing, development of single-nucleotide polymorphism markers, and identification of novel microRNAs and their targets. We present trends and advances in NGS technology in relation to Brassica crop improvement, with wide application for sophisticated genomics research into agronomically important polyploid crops.
Keyword Polyploidy
Next-generation sequencing
Brassica
Single-nucleotide polymorphism (SNP)
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

Document type: Journal Article
Sub-type: Critical review of research, literature review, critical commentary
Collections: School of Agriculture and Food Sciences
Official 2014 Collection
 
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Citation counts: TR Web of Science Citation Count  Cited 6 times in Thomson Reuters Web of Science Article | Citations
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