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

Expression and Molecular Evolution of Two DREB1 Genes in Black Poplar (Populus nigra)

(2014) Yanguang Chu et al.   PLoS One

Developing market class specific InDel markers from next generation sequence data in Phaseolus vulgaris L.

(2014) Samira Mafi Moghaddam et al.   Frontiers in Plant Science

Association of allelic variation in xylem genes with wood properties in Eucalyptus nitens

(2013) S. G. Southerton et al.   AUSTRALIAN FORESTRY

The significance of single nucleotide polymorphisms (SNPs) in Eucalyptus globulus breeding programs

(2013) Saravanan Thavamanikumar et al.   AUSTRALIAN FORESTRY

High levels of variation in Salix lignocellulose genes revealed using poplar genomic resources

(2013) Aude C Perdereau et al.   Biotechnology for Biofuels

A SNP resource for Douglas-fir: de novo transcriptome assembly and SNP detection and validation

(2013) Glenn T Howe et al.   BMC GENOMICS

Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations

(2013) Florian Jupe et al.   PLANT JOURNAL

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

(2013) Hilal Betul Kaya et al.   PLoS One

A High-Density Gene Map of Loblolly Pine ( Pinus taeda L.) Based on Exome Sequence Capture Genotyping

(2013) Leandro Gomide Neves et al.   G3-Genes Genomes Genetics

Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

(2013) Jacob A. Tennessen et al.   G3-Genes Genomes Genetics

Development of indel markers from Citrus clementina (Rutaceae) BAC-end sequences and interspecific transferability in Citrus

(2012) F. Ollitrault et al.   AMERICAN JOURNAL OF BOTANY

Targeted enrichment of the black cottonwood (Populus trichocarpa) gene space using sequence capture

(2012) Lecong Zhou et al.   BMC GENOMICS

Transcriptome sequencing of Eucalyptus camaldulensis seedlings subjected to water stress reveals functional single nucleotide polymorphisms and genes under selection

(2012) Bala R Thumma et al.   BMC GENOMICS

Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa

(2012) Ruibo Hu et al.   BMC PLANT BIOLOGY

Combining SNP discovery from next-generation sequencing data with bulked segregant analysis (BSA) to fine-map genes in polyploid wheat

(2012) Martin Trick et al.   BMC PLANT BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The Class II KNOX gene KNAT7 negatively regulates secondary wall formation in Arabidopsis and is functionally conserved in Populus

(2012) Eryang Li et al.   NEW PHYTOLOGIST

Genomic selection for growth and wood quality in Eucalyptus: capturing the missing heritability and accelerating breeding for complex traits in forest trees

(2012) Marcos D. V. Resende et al.   NEW PHYTOLOGIST

A population model for genotyping indels from next-generation sequence data

(2012) Haojing Shao et al.   NUCLEIC ACIDS RESEARCH

Targeted re-sequencing of the allohexaploid wheat exome

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

High-throughput and parallel SNP discovery in selected candidate genes inEucalyptus camaldulensisusing Illumina NGS platform

(2012) Prasad S. Hendre et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide SNP Detection, Validation, and Development of an 8K SNP Array for Apple

(2012) David Chagné et al.   PLoS One

Development and mapping of SNP assays in allotetraploid cotton

(2012) Robert L. Byers et al.   THEORETICAL AND APPLIED GENETICS

Progress in Myrtaceae genetics and genomics: Eucalyptus as the pivotal genus

(2012) Dario Grattapaglia et al.   Tree Genetics & Genomes

De novo assembled expressed gene catalog of a fast-growing Eucalyptus tree produced by Illumina mRNA-Seq

(2011) Eshchar Mizrachi et al.   BMC GENOMICS

RNA-Seq reveals genotype-specific molecular responses to water deficit in eucalyptus

(2011) Emilie Villar et al.   BMC GENOMICS

Advancing Eucalyptus genomics: identification and sequencing of lignin biosynthesis genes from deep-coverage BAC libraries

(2011) Jorge AP Paiva et al.   BMC GENOMICS

Identification of lignin genes and regulatory sequences involved in secondary cell wall formation in Acacia auriculiformis and Acacia mangium via de novo transcriptome sequencing

(2011) Melissa ML Wong et al.   BMC GENOMICS

Single nucleotide polymorphism discovery in elite north american potato germplasm

(2011) John P Hamilton et al.   BMC GENOMICS

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

(2011) Dario Grattapaglia et al.   BMC PLANT BIOLOGY

High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

(2011) Yongle Li et al.   BMC PLANT BIOLOGY

The molecular basis of quantitative variation in foliar secondary metabolites in Eucalyptus globulus

(2011) Carsten Külheim et al.   NEW PHYTOLOGIST

Survey of the genetic information carried in the genome of Eucalyptus camaldulensis

(2011) Hideki Hirakawa et al.   Plant Biotechnology

Transcript-specific, single-nucleotide polymorphism discovery and linkage analysis in hexaploid bread wheat (Triticum aestivum L.)

(2011) Alexandra M. Allen et al.   PLANT BIOTECHNOLOGY JOURNAL

Identification of candidate genes in Arabidopsis and Populus cell wall biosynthesis using text-mining, co-expression network analysis and comparative genomics

(2011) Xiaohan Yang et al.   PLANT SCIENCE

Species Discrimination, Population Structure and Linkage Disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis Using SSR Markers

(2011) Shanmugapriya Arumugasundaram et al.   PLoS One

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

Large-Scale Co-Expression Approach to Dissect Secondary Cell Wall Formation Across Plant Species

(2011) Colin Ruprecht et al.   Frontiers in Plant Science

Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome

(2011) Cyrille Saintenac et al.   GENOME BIOLOGY

SNP discovery by high-throughput sequencing in soybean

(2010) Xiaolei Wu et al.   BMC GENOMICS

High-throughput SNP discovery through deep resequencing of a reduced representation library to anchor and orient scaffolds in the soybean whole genome sequence

(2010) David L Hyten et al.   BMC GENOMICS

Transcriptional regulation of vascular cell fates

(2010) Kyoko Ohashi-Ito et al.   CURRENT OPINION IN PLANT BIOLOGY

Multiplex Target Enrichment Using DNA Indexing for Ultra-High Throughput SNP Detection

(2010) E. M. Kenny et al.   DNA RESEARCH

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood (Populus trichocarpa, Salicaceae) secondary xylem

(2010) Jill L. Wegrzyn et al.   NEW PHYTOLOGIST

Accurate SNP and mutation detection by targeted custom microarray-based genomic enrichment of short-fragment sequencing libraries

(2010) Michal Mokry et al.   NUCLEIC ACIDS RESEARCH

The DUF579 domain containing proteins IRX15 and IRX15-L affect xylan synthesis in Arabidopsis

(2010) Jacob K. Jensen et al.   PLANT JOURNAL

A high-density Diversity Arrays Technology (DArT) microarray for genome-wide genotyping in Eucalyptus

(2010) Carolina P Sansaloni et al.   Plant Methods

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Comparative SNP diversity among four Eucalyptus species for genes from secondary metabolite biosynthetic pathways

(2009) Carsten Külheim et al.   BMC GENOMICS

A new genomic resource dedicated to wood formation in Eucalyptus

(2009) David Rengel et al.   BMC PLANT BIOLOGY

The emergence of whole genome association scans in barley

(2009) Robbie Waugh et al.   CURRENT OPINION IN PLANT BIOLOGY

Global Analysis of Allele-Specific Expression in Arabidopsis thaliana

(2009) Xu Zhang et al.   GENETICS

Development of single nucleotide polymorphism (SNP) markers for use in commercial maize (Zea mays L.) germplasm

(2009) Elizabeth Jones et al.   MOLECULAR BREEDING

Hybrid selection of discrete genomic intervals on custom-designed microarrays for massively parallel sequencing

(2009) Emily Hodges et al.   Nature Protocols

Genetic diversity analysis in a seed orchard of Eucalyptus tereticornis

(2009) P. Chezhian et al.   NEW FORESTS

Towards a Systems Approach for Lignin Biosynthesis in Populus trichocarpa: Transcript Abundance and Specificity of the Monolignol Biosynthetic Genes

(2009) Rui Shi et al.   PLANT AND CELL PHYSIOLOGY

Analyses ofGA20ox- andGID1-over-expressing aspen suggest that gibberellins play two distinct roles in wood formation

(2009) Mélanie Mauriat et al.   PLANT JOURNAL

A consensus genetic map of cowpea [Vigna unguiculata (L) Walp.] and synteny based on EST-derived SNPs

(2009) W. Muchero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evaluation of next generation sequencing platforms for population targeted sequencing studies

(2009) Olivier Harismendy et al.   GENOME BIOLOGY

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce

(2008) Nathalie Pavy et al.   BMC GENOMICS

High-throughput gene and SNP discovery in Eucalyptus grandis, an uncharacterized genome

(2008) Evandro Novaes et al.   BMC GENOMICS

Generation and analysis of an Eucalyptus globulus cDNA library constructed from seedlings subjected to low temperature conditions

(2008) Susana Rasmussen-Poblete et al.   ELECTRONIC JOURNAL OF BIOTECHNOLOGY

Next-generation genetics in plants

(2008) Magnus Nordborg et al.   NATURE

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Cytokinin signaling regulates cambial development in poplar

(2008) K. Nieminen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and functional annotation of an 11,303-EST collection from Eucalyptus for studies of cold tolerance

(2008) Guylaine Keller et al.   Tree Genetics & Genomes

High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine (Pinus taeda L.)

(2008) Andrew J. Eckert et al.   Tree Genetics & Genomes

The impact of next-generation sequencing technology on genetics

(2008) Elaine R. Mardis   TRENDS IN GENETICS