The Rhododendron Genome and Chromosomal Organization Provide Insight into Shared Whole-Genome Duplications across the Heath Family (Ericaceae)

WGDdetector: a pipeline for detecting whole genome duplication events using the genome or transcriptome annotations

(2019) Yongzhi Yang et al.   BMC BIOINFORMATICS

Impact of whole-genome duplication events on diversification rates in angiosperms

(2018) Jacob B. Landis et al.   AMERICAN JOURNAL OF BOTANY

A manually annotated Actinidia chinensis var. chinensis (kiwifruit) genome highlights the challenges associated with draft genomes and gene prediction in plants

(2018) Sarah M. Pilkington et al.   BMC GENOMICS

Physiological and transcriptomic analysis revealed the involvement of crucial factors in heat stress response of Rhododendron hainanense

(2018) Ying Zhao et al.   GENE

De novo transcriptome analysis of Rhododendron molle G. Don flowers by Illumina sequencing

(2018) Zheng Xiao et al.   Genes & Genomics

Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

(2018) Shruti Choudhary et al.   GENOME

Phylogeny, historical biogeography, and diversification of angiosperm order Ericales suggest ancient Neotropical and East Asian connections

(2018) Jeffrey P. Rose et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Widespread Whole Genome Duplications Contribute to Genome Complexity and Species Diversity in Angiosperms

(2018) Ren Ren et al.   Molecular Plant

Draft genome sequence ofCamellia sinensisvar.sinensisprovides insights into the evolution of the tea genome and tea quality

(2018) Chaoling Wei et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of novel EST-SSR markers for Rhododendron longipedicellatum (Ericaceae) and cross-amplification in two congeners

(2018) Taiqiang Li et al.   Applications in Plant Sciences

Transcriptome analysis and identification of genes associated with flower development in Rhododendron pulchrum Sweet (Ericaceae)

(2018) Shuzhen Wang et al.   GENE

wgd—simple command line tools for the analysis of ancient whole-genome duplications

(2018) Arthur Zwaenepoel et al.   BIOINFORMATICS

The Tea Tree Genome Provides Insights into Tea Flavor and Independent Evolution of Caffeine Biosynthesis

(2017) En-Hua Xia et al.   Molecular Plant

MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets

(2017) Martin Steinegger et al.   NATURE BIOTECHNOLOGY

De novo RNA sequencing transcriptome of Rhododendron obtusum identified the early heat response genes involved in the transcriptional regulation of photosynthesis

(2017) Linchuan Fang et al.   PLoS One

De novo assembly of transcriptome from Rhododendron latoucheae Franch. using Illumina sequencing and development of new EST-SSR markers for genetic diversity analysis in Rhododendron

(2017) Wen Xing et al.   Tree Genetics & Genomes

Construction of a High-Density American Cranberry ( Vaccinium macrocarpon Ait.) Composite Map Using Genotyping-by-Sequencing for Multi-pedigree Linkage Mapping

(2017) Brandon Schlautman et al.   G3-Genes Genomes Genetics

De Novo Assembly of Transcriptome and Development of Novel EST-SSR Markers in Rhododendron rex Lévl. through Illumina Sequencing

(2017) Yue Zhang et al.   Frontiers in Plant Science

The draft genome assembly of Rhododendron delavayi Franch. var. delavayi

(2017) Lu Zhang et al.   GigaScience

High-Density Genetic Linkage Map Construction and Quantitative Trait Locus Mapping for Hawthorn (Crataegus pinnatifida Bunge)

(2017) Yuhui Zhao et al.   Scientific Reports

De novo SNP discovery and genetic linkage mapping in poplar using restriction site associated DNA and whole-genome sequencing technologies

(2016) Mohaddeseh Mousavi et al.   BMC GENOMICS

Expansion of the Gene Ontology knowledgebase and resources

(2016)   NUCLEIC ACIDS RESEARCH

InterPro in 2017—beyond protein family and domain annotations

(2016) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

A High-Density SNP Genetic Linkage Map and QTL Analysis of Growth-Related Traits in a Hybrid Family of Oysters ( Crassostrea gigas × Crassostrea angulata ) Using Genotyping-by-Sequencing

(2016) Jinpeng Wang et al.   G3-Genes Genomes Genetics

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand

(2015) Haibao Tang et al.   Genome Biology and Evolution

Development of a high-density cranberry SSR linkage map for comparative genetic analysis and trait detection

(2015) Brandon Schlautman et al.   MOLECULAR BREEDING

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq analysis and annotation of a draft blueberry genome assembly identifies candidate genes involved in fruit ripening, biosynthesis of bioactive compounds, and stage-specific alternative splicing

(2015) Vikas Gupta et al.   GigaScience

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

The American cranberry: first insights into the whole genome of a species adapted to bog habitat

(2014) James Polashock et al.   BMC PLANT BIOLOGY

In vitro, long-range sequence information for de novo genome assembly via transposase contiguity

(2014) Andrew Adey et al.   GENOME RESEARCH

Patterns of simple sequence repeats in cultivated blueberries (Vaccinium section Cyanococcus spp.) and their use in revealing genetic diversity and population structure

(2014) Yang Bian et al.   MOLECULAR BREEDING

Haplotype-resolved whole-genome sequencing by contiguity-preserving transposition and combinatorial indexing

(2014) Sasan Amini et al.   NATURE GENETICS

As old as the mountains: the radiations of the Ericaceae

(2014) Orlando Schwery et al.   NEW PHYTOLOGIST

Genetic Mapping and QTL Analysis of Growth-Related Traits in Pinctada fucata Using Restriction-Site Associated DNA Sequencing

(2014) Yaoguo Li et al.   PLoS One

Data access for the 1,000 Plants (1KP) project

(2014) Naim Matasci et al.   GigaScience

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

MAKER-P: A Tool Kit for the Rapid Creation, Management, and Quality Control of Plant Genome Annotations

(2013) M. S. Campbell et al.   PLANT PHYSIOLOGY

Draft genome of the kiwifruit Actinidia chinensis

(2013) Shengxiong Huang et al.   Nature Communications

Image analysis for QTL mapping of flower colour and leaf characteristics in pot azalea (Rhododendron simsii hybrids)

(2012) Ellen De Keyser et al.   EUPHYTICA

Finished bacterial genomes from shotgun sequence data

(2012) F. J. Ribeiro et al.   GENOME RESEARCH

Gamma Paleohexaploidy in the Stem Lineage of Core Eudicots: Significance for MADS-Box Gene and Species Diversification

(2012) Dries Vekemans et al.   MOLECULAR BIOLOGY AND EVOLUTION

A genome triplication associated with early diversification of the core eudicots

(2012) Yuannian Jiao et al.   GENOME BIOLOGY

A novel hybrid gene prediction method employing protein multiple sequence alignments

(2011) Oliver Keller et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

REVIGO Summarizes and Visualizes Long Lists of Gene Ontology Terms

(2011) Fran Supek et al.   PLoS One

Stacks : Building and Genotyping Loci De Novo From Short-Read Sequences

(2011) Julian M. Catchen et al.   G3-Genes Genomes Genetics

Accelerated Profile HMM Searches

(2011) Sean R. Eddy   PLoS Computational Biology

Unusual patterns of hybridization involving a narrow endemic Rhododendron species (Ericaceae) in Yunnan, China

(2010) Yongpeng Ma et al.   AMERICAN JOURNAL OF BOTANY

Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales

(2010) Tao Shi et al.   ANNALS OF BOTANY

Multipoint-likelihood maximization mapping on 4 segregating populations to achieve an integrated framework map for QTL analysis in pot azalea (Rhododendron simsii hybrids)

(2010) Ellen De Keyser et al.   BMC MOLECULAR BIOLOGY

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

Multiple Paleopolyploidizations during the Evolution of the Compositae Reveal Parallel Patterns of Duplicate Gene Retention after Millions of Years

(2008) M. S. Barker et al.   MOLECULAR BIOLOGY AND EVOLUTION

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

The Value of Nonmodel Genomes and an Example Using SynMap Within CoGe to Dissect the Hexaploidy that Predates the Rosids

(2008) Eric Lyons et al.   Tropical Plant Biology