Chromosome‐level genome assembly and population genetic analysis of a critically endangered rhododendron provide insights into its conservation

Chromosome-level genome assembly of a parent species of widely cultivated azaleas

(2020) Fu-Sheng Yang et al.   Nature Communications

Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs

(2020) Detuan Liu et al.   Frontiers in Genetics

Haplotype-phased genome and evolution of phytonutrient pathways of tetraploid blueberry

(2019) Marivi Colle et al.   GigaScience

A new species of Rhododendron (Ericaceae) from northeastern Yunnan, China

(2019) XIAO-LING TIAN et al.   Phytotaxa

Genomic signatures of extensive inbreeding in Isle Royale wolves, a population on the threshold of extinction

(2019) Jacqueline A. Robinson et al.   Science Advances

The type of bottleneck matters: Insights into the deleterious variation landscape of small managed populations

(2019) Chiara Bortoluzzi et al.   Evolutionary Applications

NextPolish: a fast and efficient genome polishing tool for long-read assembly

(2019) Jiang Hu et al.   BIOINFORMATICS

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

(2019) Valerie L Soza et al.   Genome Biology and Evolution

Genome-wide analysis of Cushion willow provides insights into alpine plant divergence in a biodiversity hotspot

(2019) Jia-hui Chen et al.   Nature Communications

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

ASTRAL-III: polynomial time species tree reconstruction from partially resolved gene trees

(2018) Chao Zhang et al.   BMC BIOINFORMATICS

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

The genetic architecture of floral traits in the woody plant Prunus mume

(2018) Qixiang Zhang et al.   Nature Communications

Rediscovery and conservation of the Critically Endangered Rhododendron griersonianum in Yunnan, China

(2018) Detuan Liu et al.   ORYX

Genomic effects of population collapse in a critically endangered ironwood tree Ostrya rehderiana

(2018) Yongzhi Yang et al.   Nature Communications

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Demographically idiosyncratic responses to climate change and rapid Pleistocene diversification of the walnut genus Juglans (Juglandaceae) revealed by whole-genome sequences

(2017) Wei-Ning Bai et al.   NEW PHYTOLOGIST

LTR_retriever: A Highly Accurate and Sensitive Program for Identification of Long Terminal Repeat Retrotransposons

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

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

(2017) Lu Zhang et al.   GigaScience

Recombination Rate Variation, Hitchhiking, and Demographic History Shape Deleterious Load in Poplar

(2016) M. Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Variation in Linked Selection and Recombination Drive Genomic Divergence during Allopatric Speciation of European and American Aspens

(2016) Jing Wang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Role of Deleterious Substitutions in Crop Genomes

(2016) Thomas J. Y. Kono et al.   MOLECULAR BIOLOGY AND EVOLUTION

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Redundans: an assembly pipeline for highly heterozygous genomes

(2016) Leszek P. Pryszcz et al.   NUCLEIC ACIDS RESEARCH

Connectivity rescues genetic diversity after a demographic bottleneck in a butterfly population network

(2016) Maryam Jangjoo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Constraint on the penultimate glacial maximum Northern Hemisphere ice topography (≈140 kyrs BP)

(2016) Florence Colleoni et al.   QUATERNARY SCIENCE REVIEWS

Strong reproductive isolation despite occasional hybridization between a widely distributed and a narrow endemic Rhododendron species

(2016) Yong-Peng Ma et al.   Scientific Reports

Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments

(2016) Neva C. Durand et al.   Cell Systems

Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom

(2016) Neva C. Durand et al.   Cell Systems

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Vegetation, fire, and climate history during the last 18 500 cal a BP in south-western Yunnan Province, China

(2015) Xiayun Xiao et al.   JOURNAL OF QUATERNARY SCIENCE

Exploring population size changes using SNP frequency spectra

(2015) Xiaoming Liu et al.   NATURE GENETICS

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

The conservation of Rhododendrons is of greater urgency than has been previously acknowledged in China

(2014) Yongpeng Ma et al.   BIODIVERSITY AND CONSERVATION

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

ANGSD: Analysis of Next Generation Sequencing Data

(2014) Thorfinn Sand Korneliussen et al.   BMC BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Fast and sensitive protein alignment using DIAMOND

(2014) Benjamin Buchfink et al.   NATURE METHODS

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Conserving plant species with extremely small populations (PSESP) in China

(2013) Yongpeng Ma et al.   BIODIVERSITY AND CONSERVATION

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Robust Demographic Inference from Genomic and SNP Data

(2013) Laurent Excoffier et al.   PLoS Genetics

Hi–C: A comprehensive technique to capture the conformation of genomes

(2012) Jon-Matthew Belton et al.   METHODS

SIFT web server: predicting effects of amino acid substitutions on proteins

(2012) Ngak-Leng Sim et al.   NUCLEIC ACIDS RESEARCH

Predicting the Functional Effect of Amino Acid Substitutions and Indels

(2012) Yongwook Choi et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

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

(2011) Carson Holt et al.   BMC BIOINFORMATICS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genomic Runs of Homozygosity Record Population History and Consanguinity

(2010) Mirna Kirin et al.   PLoS One

Quantitative measures for the management and comparison of annotated genomes

(2009) Karen Eilbeck et al.   BMC BIOINFORMATICS

Ecological Change, Range Fluctuations and Population Dynamics during the Pleistocene

(2009) Michael Hofreiter et al.   CURRENT BIOLOGY

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS