Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Identification, characterization, validation and cross-species amplification of genic-SSRs in Indian Mustard (Brassica juncea)

(2016) Binay K. Singh et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

Mobile small RNAs regulate genome-wide DNA methylation

(2016) Mathew G. Lewsey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

De NovoTranscriptome Sequencing ofOlea europaeaL. to Identify Genes Involved in the Development of the Pollen Tube

(2016) Domenico Iaria et al.   TheScientificWorldJOURNAL

MicroRNAs in Rice Innate Immunity

(2016) Patricia Baldrich et al.   Rice

Transcriptome sequencing of Crucihimalaya himalaica (Brassicaceae) reveals how Arabidopsis close relative adapt to the Qinghai-Tibet Plateau

(2016) Qin Qiao et al.   Scientific Reports

Exploiting the Repetitive Fraction of the Wheat Genome for High-Throughput Single-Nucleotide Polymorphism Discovery and Genotyping

(2016) Nelly Cubizolles et al.   Plant Genome

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

De NovoTranscriptome Sequencing ofOlea europaeaL. to Identify Genes Involved in the Development of the Pollen Tube

(2016) Domenico Iaria et al.   Scientific World Journal

Comparative analysis of sugarcane bagasse metagenome reveals unique and conserved biomass-degrading enzymes among lignocellulolytic microbial communities

(2015) Wuttichai Mhuantong et al.   Biotechnology for Biofuels

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Characterization of miRNAs associated with Botrytis cinerea infection of tomato leaves

(2015) Weibo Jin et al.   BMC PLANT BIOLOGY

Transcriptome analysis in Cucumis sativus identifies genes involved in multicellular trichome development

(2015) Jun-Long Zhao et al.   GENOMICS

Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS)

(2015) Wirulda Pootakham et al.   GENOMICS

De Novo Transcriptome Sequencing of Low Temperature-Treated Phlox subulata and Analysis of the Genes Involved in Cold Stress

(2015) Yanting Qu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Development and Characterization of Polymorphic Genic-SSR Markers in Larix kaempferi

(2015) Xing-Bin Chen et al.   MOLECULES

G&T-seq: parallel sequencing of single-cell genomes and transcriptomes

(2015) Iain C Macaulay et al.   NATURE METHODS

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

Identification and characterisation of tobacco microRNA transcriptome using high-throughput sequencing

(2015) J. Gao et al.   PLANT BIOLOGY

Transcriptome dynamics of developing maize leaves and genomewide prediction ofciselements and their cognate transcription factors

(2015) Chun-Ping Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Third generation sequencing: technology and its potential impact on evolutionary biodiversity research

(2015) Christoph Bleidorn   SYSTEMATICS AND BIODIVERSITY

Single-Cell DNA Methylome Sequencing and Bioinformatic Inference of Epigenomic Cell-State Dynamics

(2015) Matthias Farlik et al.   Cell Reports

Exome Sequencing: Current and Future Perspectives

(2015) Amanda Warr et al.   G3-Genes Genomes Genetics

Development of Genetic Markers in Eucalyptus Species by Target Enrichment and Exome Sequencing

(2015) Modhumita Ghosh Dasgupta et al.   PLoS One

De Novo Assembly and Characterization of Stress Transcriptome in a Salinity-Tolerant Variety CS52 of Brassica juncea

(2015) Rita Sharma et al.   PLoS One

Development of SSR Markers and Genetic Diversity in White Birch (Betula platyphylla)

(2015) Wei Hao et al.   PLoS One

Large-Scale SNP Discovery and Genotyping for Constructing a High-Density Genetic Map of Tea Plant Using Specific-Locus Amplified Fragment Sequencing (SLAF-seq)

(2015) Jian-Qiang Ma et al.   PLoS One

Mutation Scanning in Wheat by Exon Capture and Next-Generation Sequencing

(2015) Robert King et al.   PLoS One

Molecular Karyotyping and Exome Analysis of Salt-Tolerant Rice Mutant from Somaclonal Variation

(2015) Thanikarn Udomchalothorn et al.   Plant Genome

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

Systematic genome sequence differences among leaf cells within individual trees

(2014) Deepti Diwan et al.   BMC GENOMICS

RNA sequencing-mediated transcriptome analysis of rice plants in endoplasmic reticulum stress conditions

(2014) Yuhya Wakasa et al.   BMC PLANT BIOLOGY

The Effects of Restriction-Enzyme Choice on Properties of Genotyping-by-Sequencing Libraries: A Study in Cassava ()

(2014) Martha T. Hamblin et al.   CROP SCIENCE

Associative Transcriptomics Study Dissects the Genetic Architecture of Seed Glucosinolate Content in Brassica napus

(2014) G. Lu et al.   DNA RESEARCH

Quantitative Trait Locus Mapping and Candidate Gene Analysis for Plant Architecture Traits Using Whole Genome Re-Sequencing in Rice

(2014) Jung-Hyun Lim et al.   MOLECULES AND CELLS

MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Using next-generation sequencing to isolate mutant genes from forward genetic screens

(2014) Korbinian Schneeberger   NATURE REVIEWS GENETICS

Efficient Genome-Wide Detection and Cataloging of EMS-Induced Mutations Using Exome Capture and Next-Generation Sequencing

(2014) I. M. Henry et al.   PLANT CELL

mRNA and Small RNA Transcriptomes Reveal Insights into Dynamic Homoeolog Regulation of Allopolyploid Heterosis in Nascent Hexaploid Wheat

(2014) A. Li et al.   PLANT CELL

Single-Nucleotide Polymorphism Markers from De-Novo Assembly of the Pomegranate Transcriptome Reveal Germplasm Genetic Diversity

(2014) Ron Ophir et al.   PLoS One

Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications

(2014) Himabindu Kudapa et al.   PLoS One

Transcriptome Sequencing and De Novo Analysis of Cytoplasmic Male Sterility and Maintenance in JA-CMS Cotton

(2014) Peng Yang et al.   PLoS One

Temporal patterns of gene expression in developing maize endosperm identified through transcriptome sequencing

(2014) G. Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next Generation Sequencing: Potential and Application in Drug Discovery

(2014) Navneet Kumar Yadav et al.   TheScientificWorldJOURNAL

Ten years of next-generation sequencing technology

(2014) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Transcriptome and Complexity-Reduced, DNA-Based Identification of Intraspecies Single-Nucleotide Polymorphisms in the Polyploid Gossypium hirsutum L.

(2014) Qian-Hao Zhu et al.   G3-Genes Genomes Genetics

Single Cell Genomics: Advances and Future Perspectives

(2014) Iain C. Macaulay et al.   PLoS Genetics

Analysis of plant microbe interactions in the era of next generation sequencing technologies

(2014) Claudia Knief   Frontiers in Plant Science

The 3,000 rice genomes project

(2014)   GigaScience

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

Molecular functions of small regulatory noncoding RNA

(2013) Yong Huang et al.   BIOCHEMISTRY-MOSCOW

Identification of genome-wide single nucleotide polymorphisms in allopolyploid crop Brassica napus

(2013) Shunmou Huang et al.   BMC GENOMICS

De novo sequencing of sunflower genome for SNP discovery using RAD (Restriction site Associated DNA) approach

(2013) Venkatramana Pegadaraju et al.   BMC GENOMICS

A survey of tools for variant analysis of next-generation genome sequencing data

(2013) S. Pabinger et al.   BRIEFINGS IN BIOINFORMATICS

Development of EST-SSR markers through data mining and their use for genetic diversity study in Indian accessions of Jatropha curcas L.: a potential energy crop

(2013) Maya Kumari et al.   Genes & Genomics

Principles of transcriptome analysis and gene expression quantification: an RNA-seq tutorial

(2013) Jochen B. W. Wolf   Molecular Ecology Resources

Patterns of population epigenomic diversity

(2013) Robert J. Schmitz et al.   NATURE

Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes

(2013) Mads Albertsen et al.   NATURE BIOTECHNOLOGY

Massive genomic variation and strong selection in Arabidopsis thaliana lines from Sweden

(2013) Quan Long et al.   NATURE GENETICS

A genomic view of mosaicism and human disease

(2013) Leslie G. Biesecker et al.   NATURE REVIEWS GENETICS

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

Whole-exome targeted sequencing of the uncharacterized pine genome

(2013) Leandro G. Neves et al.   PLANT JOURNAL

An RNA Sequencing Transcriptome Analysis Reveals Novel Insights into Molecular Aspects of the Nitrate Impact on the Nodule Activity of Medicago truncatula

(2013) R. Cabeza et al.   PLANT PHYSIOLOGY

QTL Analysis Using SNP Markers Developed by Next-Generation Sequencing for Identification of Candidate Genes Controlling 4-Methylthio-3-Butenyl Glucosinolate Contents in Roots of Radish, Raphanus sativus L

(2013) Zhongwei Zou et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

De Novo Transcriptome of Brassica juncea Seed Coat and Identification of Genes for the Biosynthesis of Flavonoids

(2013) Xianjun Liu et al.   PLoS One

Mapping of Quantitative Trait Loci Underlying Cold Tolerance in Rice Seedlings via High-Throughput Sequencing of Pooled Extremes

(2013) Zemao Yang et al.   PLoS One

Comparative Transcriptome Profiling of a Resistant vs. Susceptible Tomato (Solanum lycopersicum) Cultivar in Response to Infection by Tomato Yellow Leaf Curl Virus

(2013) Tianzi Chen et al.   PLoS One

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum ; Fabaceae), a crop species without a reference genome

(2012) Sarwar Azam et al.   AMERICAN JOURNAL OF BOTANY

Quality and quantity of data recovered from massively parallel sequencing: Examples in Asparagales and Poaceae

(2012) P. Roxanne Steele et al.   AMERICAN JOURNAL OF BOTANY

Targeted sequence capture as a powerful tool for evolutionary analysis1

(2012) Corrinne E. Grover et al.   AMERICAN JOURNAL OF BOTANY

Applications of next-generation sequencing in plant biology

(2012) Ashley N. Egan et al.   AMERICAN JOURNAL OF BOTANY

Prevalence of single nucleotide polymorphism among 27 diverse alfalfa genotypes as assessed by transcriptome sequencing

(2012) Xuehui Li et al.   BMC GENOMICS

Third-generation sequencing techniques and applications to drug discovery

(2012) Fatih Ozsolak   Expert Opinion on Drug Discovery

Comparison of Next-Generation Sequencing Systems

(2012) Lin Liu et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Identification of QTLs for eight agronomically important traits using an ultra-high-density map based on SNPs generated from high-throughput sequencing in sorghum under contrasting photoperiods

(2012) Guihua Zou et al.   JOURNAL OF EXPERIMENTAL BOTANY

Tet-assisted bisulfite sequencing of 5-hydroxymethylcytosine

(2012) Miao Yu et al.   Nature Protocols

Targeted re-sequencing of the allohexaploid wheat exome

(2012) Mark O. Winfield et al.   PLANT BIOTECHNOLOGY JOURNAL

Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivumL.)

(2012) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

Transcriptome Sequencing Identifies SPL7-Regulated Copper Acquisition Genes FRO4/FRO5 and the Copper Dependence of Iron Homeostasis in Arabidopsis

(2012) M. Bernal et al.   PLANT CELL

Using next-generation sequencing approaches to isolate simple sequence repeat (SSR) loci in the plant sciences

(2011) Juan E. Zalapa et al.   AMERICAN JOURNAL OF BOTANY

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants

(2011) Stéphanie M. Swarbreck et al.   PLANT AND CELL PHYSIOLOGY

Allele mining in crops: Prospects and potentials

(2010) G. Ram Kumar et al.   BIOTECHNOLOGY ADVANCES

Transcriptome sequencing and comparative analysis of cucumber flowers with different sex types

(2010) Shaogui Guo et al.   BMC GENOMICS

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

Direct detection of DNA methylation during single-molecule, real-time sequencing

(2010) Benjamin A Flusberg et al.   NATURE METHODS

Pathogenesis, parasitism and mutualism in the trophic space of microbe–plant interactions

(2010) Adrian C. Newton et al.   TRENDS IN MICROBIOLOGY

A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers

(2009) Emma S Mace et al.   BMC PLANT BIOLOGY

Direct RNA sequencing

(2009) Fatih Ozsolak et al.   NATURE

Focus on next-generation sequencing data analysis

(2009) Nicole Rusk   NATURE METHODS

Virtual terminator nucleotides for next-generation DNA sequencing

(2009) Jayson Bowers et al.   NATURE METHODS

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

(2009) Martin Trick et al.   PLANT BIOTECHNOLOGY JOURNAL

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

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

Methyl-DNA immunoprecipitation (MeDIP): Hunting down the DNA methylome

(2008) Filipe V. Jacinto et al.   BIOTECHNIQUES

Application of massively parallel sequencing to microRNA profiling and discovery in human embryonic stem cells

(2008) R. D. Morin et al.   GENOME RESEARCH

Applications of next-generation sequencing technologies in functional genomics

(2008) Olena Morozova et al.   GENOMICS

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE

High-density genetic map of durum wheat × wild emmer wheat based on SSR and DArT markers

(2008) Zvi Peleg et al.   THEORETICAL AND APPLIED GENETICS

Genetical Genomics: Spotlight on QTL Hotspots

(2008) Rainer Breitling et al.   PLoS Genetics

Steady progress and recent breakthroughs in the accuracy of automated genome annotation

(2007) Michael R. Brent   NATURE REVIEWS GENETICS