Applications and challenges of next-generation sequencing in Brassica species

High-density SNP-based genetic map development and linkage disequilibrium assessment in Brassica napus L

(2013) Régine Delourme et al.   BMC GENOMICS

Detection and genotyping of restriction fragment associated polymorphisms in polyploid crops with a pseudo-reference sequence: a case study in allotetraploid Brassica napus

(2013) Xun Chen et al.   BMC GENOMICS

A glimpse into past, present, and future DNA sequencing

(2013) Marcos Morey et al.   MOLECULAR GENETICS AND METABOLISM

Next-generation sequencing applications for wheat crop improvement

(2012) Paul J. Berkman et al.   AMERICAN JOURNAL OF BOTANY

Designing a transcriptome next-generation sequencing project for a nonmodel plant species1

(2012) Susan R. Strickler et al.   AMERICAN JOURNAL OF BOTANY

Next-generation sequencing and genome evolution in allopolyploids

(2012) Richard J. A. Buggs et al.   AMERICAN JOURNAL OF BOTANY

An evaluation of two-channel ChIP-on-chip and DNA methylation microarray normalization strategies

(2012) Michiel E Adriaens et al.   BMC GENOMICS

Use of mRNA-seq to discriminate contributions to the transcriptome from the constituent genomes of the polyploid crop species Brassica napus

(2012) Janet Higgins et al.   BMC GENOMICS

High-throughput polymorphism detection and genotyping in Brassica napus using next-generation RAD sequencing

(2012) Anja Bus et al.   BMC GENOMICS

Transcriptome analysis of stem development in the tumourous stem mustard Brassica juncea var. tumida Tsen et Lee by RNA sequencing

(2012) Quan Sun et al.   BMC PLANT BIOLOGY

Molecular Tools for Exploring Polyploid Genomes in Plants

(2012) Riccardo Aversano et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Application of large-scale sequencing to marker discovery in plants

(2012) Robert J Henry et al.   JOURNAL OF BIOSCIENCES

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

(2012) Zhao Sheng Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification and profiling of arsenic stress-induced microRNAs inBrassica juncea

(2012) Sudhakar Srivastava et al.   JOURNAL OF EXPERIMENTAL BOTANY

High-throughput sequencing discovery of conserved and novel microRNAs in Chinese cabbage (Brassica rapa L. ssp. pekinensis)

(2012) Fengde Wang et al.   MOLECULAR GENETICS AND GENOMICS

New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica Species

(2012) Lijuan Wei et al.   Molecular Plant

Analysis of the bread wheat genome using whole-genome shotgun sequencing

(2012) Rachel Brenchley et al.   NATURE

Associative transcriptomics of traits in the polyploid crop species Brassica napus

(2012) Andrea L Harper et al.   NATURE BIOTECHNOLOGY

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

The draft genome of sweet orange (Citrus sinensis)

(2012) Qiang Xu et al.   NATURE GENETICS

Associative transcriptomics

(2012) Hannah Stower   NATURE REVIEWS GENETICS

Identification and characterization of candidateRlm4blackleg resistance genes inBrassica napususing next-generation sequencing

(2012) Reece Tollenaere et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

(2012) Gopala K. Subbaiyan et al.   PLANT BIOTECHNOLOGY JOURNAL

Potential to improve oilseed rape and canola breeding in the genomics era

(2012) Rod J. Snowdon et al.   PLANT BREEDING

Development and application of single nucleotide polymorphism markers in the polyploid Brassica napus by 454 sequencing of expressed sequence tags

(2012) Zhiyong Hu et al.   PLANT BREEDING

Comparative Analysis of Syntenic Genes in Grass Genomes Reveals Accelerated Rates of Gene Structure and Coding Sequence Evolution in Polyploid Wheat

(2012) E. D. Akhunov et al.   PLANT PHYSIOLOGY

Evaluating Characteristics of De Novo Assembly Software on 454 Transcriptome Data: A Simulation Approach

(2012) Marvin Mundry et al.   PLoS One

Discovery of Pod Shatter-Resistant Associated SNPs by Deep Sequencing of a Representative Library Followed by Bulk Segregant Analysis in Rapeseed

(2012) Zhiyong Hu et al.   PLoS One

Identifying Conserved and Novel MicroRNAs in Developing Seeds of Brassica napus Using Deep Sequencing

(2012) Ana Paula Körbes et al.   PLoS One

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Alternative splicing in plants – coming of age

(2012) Naeem H. Syed et al.   TRENDS IN PLANT SCIENCE

R453Plus1Toolbox: an R/Bioconductor package for analyzing Roche 454 Sequencing data

(2011) Hans-Ulrich Klein et al.   BIOINFORMATICS

De novo assembly and characterization of root transcriptome using Illumina paired-end sequencing and development of cSSR markers in sweetpotato (Ipomoea batatas)

(2011) Zhangying Wang et al.   BMC GENOMICS

A novel class of heat-responsive small RNAs derived from the chloroplast genome of Chinese cabbage (Brassica rapa)

(2011) Lu Wang et al.   BMC GENOMICS

Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis)

(2011) Xiangjun Zhou et al.   BMC PLANT BIOLOGY

Development of genome-wide SNP assays for rice

(2011) Susan R. McCouch et al.   BREEDING SCIENCE

Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa

(2011) Xiang Yu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

De novo genome sequencing and comparative genomics of date palm (Phoenix dactylifera)

(2011) Eman K Al-Dous et al.   NATURE BIOTECHNOLOGY

Dissecting the genome of the polyploid crop oilseed rape by transcriptome sequencing

(2011) Ian Bancroft et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

454 EST analysis detects genes putatively involved in ginsenoside biosynthesis in Panax ginseng

(2011) S. Chen et al.   PLANT CELL REPORTS

Comparative deep transcriptional profiling of four developing oilseeds

(2011) Manuel A. Troncoso-Ponce et al.   PLANT JOURNAL

Transcriptome Profiling of Dehydration Stress in the Chinese Cabbage (Brassica rapa L. ssp. pekinensis) by Tag Sequencing

(2011) Shuancang Yu et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genetic Architecture of Maize Kernel Composition in the Nested Association Mapping and Inbred Association Panels

(2011) J. P. Cook et al.   PLANT PHYSIOLOGY

Small RNA Profiling in Two Brassica napus Cultivars Identifies MicroRNAs with Oil Production- and Development-Correlated Expression and New Small RNA Classes

(2011) Y.-T. Zhao et al.   PLANT PHYSIOLOGY

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

(2011) J. A. Poland et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive changes to alternative splicing patterns following allopolyploidy in natural and resynthesized polyploids

(2011) R. Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of genome-wide selection efficiency in maize nested association mapping populations

(2011) Zhigang Guo et al.   THEORETICAL AND APPLIED GENETICS

Single-molecule direct RNA sequencing without cDNA synthesis

(2011) Fatih Ozsolak et al.   Wiley Interdisciplinary Reviews-RNA

Full genome re-sequencing reveals a novel circadian clock mutation in Arabidopsis

(2011) Kevin Ashelford et al.   GENOME BIOLOGY

Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems

(2011) André E Minoche et al.   GENOME BIOLOGY

Construction of an integrated genetic linkage map for the A genome of Brassica napus using SSR markers derived from sequenced BACs in B. rapa

(2010) Jinsong Xu et al.   BMC GENOMICS

Association mapping of seed oil content in Brassica napus and comparison with quantitative trait loci identified from linkage mappingThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Jun Zou et al.   GENOME

SNP discovery by amplicon sequencing and multiplex SNP genotyping in the allopolyploid species Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) G. Durstewitz et al.   GENOME

Prospects and challenges for genome-wide association and genomic selection in oilseed Brassica speciesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”

(2010) W.A. Cowling et al.   GENOME

Association mapping for phenological, morphological, and quality traits in canola quality winter rapeseed (Brassica napus L.)This article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Nora Honsdorf et al.   GENOME

Design of a Brassica rapa core collection for association mapping studiesThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Jianjun Zhao et al.   GENOME

Towards unambiguous transcript mapping in the allotetraploid Brassica napusThis article is one of a selection of papers from the conference “Exploiting Genome-wide Association in Oilseed Brassicas: a model for genetic improvement of major OECD crops for sustainable farming”.

(2010) Isobel A.P. Parkin et al.   GENOME

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Rapid divergence of repetitive DNAs in Brassica relatives

(2010) Dal-Hoe Koo et al.   GENOMICS

Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis

(2010) Sergio E. Baranzini et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome sequencing and analysis of the model grass Brachypodium distachyon

(2010) John P. Vogel et al.   NATURE

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Identification of a Spontaneous Frame Shift Mutation in a Nonreference Arabidopsis Accession Using Whole Genome Sequencing

(2010) R. A. E. Laitinen et al.   PLANT PHYSIOLOGY

A Brassica Exon Array for Whole-Transcript Gene Expression Profiling

(2010) Christopher G. Love et al.   PLoS One

Sequence and structure of Brassica rapa chromosome A3

(2010) Jeong-Hwan Mun et al.   GENOME BIOLOGY

Gene expression profiling via LongSAGE in a non-model plant species: a case study in seeds of Brassica napus

(2009) Christian Obermeier et al.   BMC GENOMICS

A newly-developed community microarray resource for transcriptome profiling in Brassica species enables the confirmation of Brassica-specific expressed sequences

(2009) Martin Trick et al.   BMC PLANT BIOLOGY

A Brassica rapa Linkage Map of EST-based SNP Markers for Identification of Candidate Genes Controlling Flowering Time and Leaf Morphological Traits

(2009) F. Li et al.   DNA RESEARCH

The sequence and de novo assembly of the giant panda genome

(2009) Ruiqiang Li et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Single nucleotide polymorphism (SNP) discovery in the polyploidBrassica napususing Solexa transcriptome sequencing

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

Plant genome sequencing: applications for crop improvement

(2009) David Edwards et al.   PLANT BIOTECHNOLOGY JOURNAL

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)

(2009) Q. Xia et al.   SCIENCE

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY

Small RNAs Originated from Pseudogenes: cis- or trans-Acting?

(2009) Xingyi Guo et al.   PLoS Computational Biology

Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication

(2009) Jeong-Hwan Mun et al.   GENOME BIOLOGY

The first generation of a BAC-based physical map of Brassica rapa

(2008) Jeong-Hwan Mun et al.   BMC GENOMICS

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

AutoSNPdb: an annotated single nucleotide polymorphism database for crop plants

(2008) C. Duran et al.   NUCLEIC ACIDS RESEARCH

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE