A phased genome based on single sperm sequencing reveals crossover pattern and complex relatedness in tea plants

The reference genome of tea plant and resequencing of 81 diverse accessions provide insights into genome evolution and adaptation of tea plants

(2020) Enhua Xia et al.   Molecular Plant

The Chromosome-Level Reference Genome of Tea Tree Unveils Recent Bursts of Non-autonomous LTR Retrotransposons in Driving Genome Size Evolution

(2020) Qun-Jie Zhang et al.   Molecular Plant

Ranbow: A fast and accurate method for polyploid haplotype reconstruction

(2020) M-Hossein Moeinzadeh et al.   PLoS Computational Biology

Genome assembly of wild tea tree DASZ reveals pedigree and selection history of tea varieties

(2020) Weiyi Zhang et al.   Nature Communications

MapMan4: a refined protein classification and annotation framework applicable to multi-omics data analysis

(2019) Rainer Schwacke et al.   Molecular Plant

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

(2019) Marivi Colle et al.   GigaScience

Single gametophyte sequencing reveals that crossover events differ between sexes in maize

(2019) Cheng Luo et al.   Nature Communications

Patterns of genome-wide allele-specific expression in hybrid rice and the implications on the genetic basis of heterosis

(2019) Lin Shao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Characterization of four polymorphic genes controlling red leaf color in lettuce that have undergone disruptive selection since domestication

(2019) Wenqing Su et al.   PLANT BIOTECHNOLOGY JOURNAL

Single-pollen-cell sequencing for gamete-based phased diploid genome assembly in plants

(2019) Dongqing Shi et al.   GENOME RESEARCH

Linked-read sequencing of gametes allows efficient genome-wide analysis of meiotic recombination

(2019) Hequan Sun et al.   Nature Communications

Co-transmission of Related Malaria Parasite Lineages Shapes Within-Host Parasite Diversity

(2019) Standwell C. Nkhoma et al.   Cell Host & Microbe

Meiotic Recombination: Mixing It Up in Plants

(2018) Yingxiang Wang et al.   Annual Review of Plant Biology

Efficient algorithms for polyploid haplotype phasing

(2018) Dan He et al.   BMC GENOMICS

WEGO 2.0: a web tool for analyzing and plotting GO annotations, 2018 update

(2018) Jia Ye et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of haplotype-resolved genomes with trio binning

(2018) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Tea Polyphenols in Promotion of Human Health

(2018) Naghma Khan et al.   Nutrients

Dynamic and Antagonistic Allele-Specific Epigenetic Modifications Controlling the Expression of Imprinted Genes in Maize Endosperm

(2017) Xiaomei Dong et al.   Molecular Plant

Brassica napus GLABRA3-1 promotes anthocyanin biosynthesis and trichome formation in true leaves when expressed in Arabidopsis thaliana

(2017) C. Gao et al.   PLANT BIOLOGY

Functional Analysis of Two Flavanone-3-Hydroxylase Genes from Camellia sinensis: A Critical Role in Flavonoid Accumulation

(2017) Yahui Han et al.   Genes

A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes

(2016) Naoki Nariai et al.   BMC GENOMICS

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

(2016) Kenji Yano et al.   NATURE GENETICS

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Rare variant phasing and haplotypic expression from RNA sequencing with phASER

(2016) Stephane E. Castel et al.   Nature Communications

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Fingerprinting 128 Chinese clonal tea cultivars using SSR markers provides new insights into their pedigree relationships

(2015) Li-Qiang Tan et al.   Tree Genetics & Genomes

Dissecting meiotic recombination based on tetrad analysis by single-microspore sequencing in maize

(2015) Xiang Li et al.   Nature Communications

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Topoisomerase II mediates meiotic crossover interference

(2014) Liangran Zhang et al.   NATURE

Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids

(2014) A. Paschold et al.   PLANT CELL

Relationship Estimation from Whole-Genome Sequence Data

(2014) Hong Li et al.   PLoS Genetics

Crossover Patterning by the Beam-Film Model: Analysis and Implications

(2014) Liangran Zhang et al.   PLoS Genetics

Haplotype Estimation Using Sequencing Reads

(2013) Olivier Delaneau et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Genome Analyses of Single Human Oocytes

(2013) Yu Hou et al.   CELL

Identity by Descent: Variation in Meiosis, Across Genomes, and in Populations

(2013) E. A. Thompson   GENETICS

Improving the Accuracy and Efficiency of Identity-by-Descent Detection in Population Data

(2013) B. L. Browning et al.   GENETICS

Sequencing of isolated sperm cells for direct haplotyping of a human genome

(2013) E. F. Kirkness et al.   GENOME RESEARCH

Ignoring Heterozygous Sites Biases Phylogenomic Estimates of Divergence Times: Implications for the Evolutionary History of Microtus Voles

(2013) Heidi E.L. Lischer et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

The genomic landscape of meiotic crossovers and gene conversions in Arabidopsis thaliana

(2013) Erik Wijnker et al.   eLife

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Genome-wide Single-Cell Analysis of Recombination Activity and De Novo Mutation Rates in Human Sperm

(2012) Jianbin Wang et al.   CELL

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing

(2012) S. Lu et al.   SCIENCE

CODA (crossover distribution analyzer): quantitative characterization of crossover position patterns along chromosomes

(2011) Franck Gauthier et al.   BMC BIOINFORMATICS

Analysis of Arabidopsis genome-wide variations before and after meiosis and meiotic recombination by resequencing Landsberg erecta and all four products of a single meiosis

(2011) P. Lu et al.   GENOME RESEARCH

The importance of phase information for human genomics

(2011) Ryan Tewhey et al.   NATURE REVIEWS GENETICS

Haplotype phasing: existing methods and new developments

(2011) Sharon R. Browning et al.   NATURE REVIEWS GENETICS

An early gene of the flavonoid pathway, flavanone 3-hydroxylase, exhibits a positive relationship with the concentration of catechins in tea (Camellia sinensis)

(2011) K. Singh et al.   TREE PHYSIOLOGY

Robust relationship inference in genome-wide association studies

(2010) Ani Manichaikul et al.   BIOINFORMATICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Allele-specific DNA methylation: beyond imprinting

(2010) B. Tycko   HUMAN MOLECULAR GENETICS

Fine-scale recombination rate differences between sexes, populations and individuals

(2010) Augustine Kong et al.   NATURE

Haplotype-resolved genome sequencing of a Gujarati Indian individual

(2010) Jacob O Kitzman et al.   NATURE BIOTECHNOLOGY

Direct determination of molecular haplotypes by chromosome microdissection

(2010) Li Ma et al.   NATURE METHODS

Genotype Imputation

(2009) Yun Li et al.   Annual Review of Genomics and Human Genetics

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Two Types of Meiotic Crossovers Coexist in Maize

(2009) M. Falque et al.   PLANT CELL

The endogenous GL3, but not EGL3, gene is necessary for anthocyanin accumulation as induced by nitrogen depletion in Arabidopsis rosette stage leaves

(2009) Dugassa N. Feyissa et al.   PLANTA

Whole population, genome-wide mapping of hidden relatedness

(2008) A. Gusev et al.   GENOME RESEARCH

Detection of sharing by descent, long-range phasing and haplotype imputation

(2008) Augustine Kong et al.   NATURE GENETICS

Efficient and Accurate Construction of Genetic Linkage Maps from the Minimum Spanning Tree of a Graph

(2008) Yonghui Wu et al.   PLoS Genetics