Graph-based pan-genome reveals structural and sequence variations related to agronomic traits and domestication in cucumber

BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes

(2021) Mosè Manni et al.   MOLECULAR BIOLOGY AND EVOLUTION

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Major Impacts of Widespread Structural Variation on Gene Expression and Crop Improvement in Tomato

(2020) Michael Alonge et al.   CELL

The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor

(2019) Lei Gao et al.   NATURE GENETICS

Goodbye reference, hello genome graphs

(2019) Adam Ameur   NATURE BIOTECHNOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

A comprehensive genome variation map of melon identifies multiple domestication events and loci influencing agronomic traits

(2019) Guangwei Zhao et al.   NATURE GENETICS

FLOWERING LOCUS T Improves Cucumber Adaptation to Higher Latitudes

(2019) Shenhao Wang et al.   PLANT PHYSIOLOGY

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice

(2018) Qiang Zhao et al.   NATURE GENETICS

Structural variation in the 3D genome

(2018) Malte Spielmann et al.   NATURE REVIEWS GENETICS

A CsTu -TS1 regulatory module promotes fruit tubercule formation in cucumber

(2018) Sen Yang et al.   PLANT BIOTECHNOLOGY JOURNAL

Combined fine mapping, genetic diversity, and transcriptome profiling reveals that the auxin transporter gene ns plays an important role in cucumber fruit spine development

(2018) Qing Xie et al.   THEORETICAL AND APPLIED GENETICS

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Variation graph toolkit improves read mapping by representing genetic variation in the reference

(2018) Erik Garrison et al.   NATURE BIOTECHNOLOGY

The USDA cucumber (Cucumis sativus L.) collection: genetic diversity, population structure, genome-wide association studies, and core collection development

(2018) Xin Wang et al.   Horticulture Research

Exploring and exploiting pan-genomics for crop improvement

(2018) Yongfu Tao et al.   Molecular Plant

Molecular basis of cucumber fruit domestication

(2018) Gen Che et al.   CURRENT OPINION IN PLANT BIOLOGY

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Genetic Analysis and QTL Mapping of Resistance to Gummy Stem Blight in Cucumis sativus Seedling Stage

(2017) Shulin Liu et al.   PLANT DISEASE

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

(2017) Shujun Ou et al.   PLANT PHYSIOLOGY

GenoCore: A simple and fast algorithm for core subset selection from large genotype datasets

(2017) Seongmun Jeong et al.   PLoS One

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Transient structural variations have strong effects on quantitative traits and reproductive isolation in fission yeast

(2017) Daniel C. Jeffares et al.   Nature Communications

Analysis of Plant Pan-Genomes and Transcriptomes with GET_HOMOLOGUES-EST, a Clustering Solution for Sequences of the Same Species

(2017) Bruno Contreras-Moreira et al.   Frontiers in Plant Science

A fragment substitution in the promoter of CsHDZIV11/CsGL3 is responsible for fruit spine density in cucumber (Cucumis sativus L.)

(2016) Haiyang Zhang et al.   THEORETICAL AND APPLIED GENETICS

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

(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

The identification of Cucumis sativus Glabrous 1 (CsGL1) required for the formation of trichomes uncovers a novel function for the homeodomain-leucine zipper I gene

(2015) Qiang Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

A Sequencing-Based Linkage Map of Cucumber

(2015) Qian Zhou et al.   Molecular Plant

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Towards plant pangenomics

(2015) Agnieszka A. Golicz et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

ALLMAPS: robust scaffold ordering based on multiple maps

(2015) Haibao Tang et al.   GENOME BIOLOGY

InterProScan 5: genome-scale protein function classification

(2014) P. Jones et al.   BIOINFORMATICS

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

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

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Tuberculate fruit geneTuencodes a C2H2zinc finger protein that is required for the warty fruit phenotype in cucumber (Cucumis sativusL.)

(2014) Xuqin Yang et al.   PLANT JOURNAL

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

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

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

Protein intrinsic disorder in plants

(2013) Florencio Pazos et al.   Frontiers in Plant Science

DELLY: structural variant discovery by integrated paired-end and split-read analysis

(2012) T. Rausch et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2012) Jon-Matthew Belton et al.   METHODS

The protein kinase Pstol1 from traditional rice confers tolerance of phosphorus deficiency

(2012) Rico Gamuyao et al.   NATURE

Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly

(2012) Luming Yang et al.   PLANT JOURNAL

Syntenic gene analysis between Brassica rapa and other Brassicaceae species

(2012) Feng Cheng et al.   Frontiers in Plant Science

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

PELPK1 (At5g09530) contains a unique pentapeptide repeat and is a positive regulator of germination in Arabidopsis thaliana

(2011) Abdur Rashid et al.   PLANT CELL REPORTS

Construction of a high density integrated genetic map for cucumber (Cucumis sativus L.)

(2011) Wei-Wei Zhang et al.   THEORETICAL AND APPLIED GENETICS

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Molecular Isolation of the M Gene Suggests That a Conserved-Residue Conversion Induces the Formation of Bisexual Flowers in Cucumber Plants

(2009) Zheng Li et al.   GENETICS

Building the sequence map of the human pan-genome

(2009) Ruiqiang Li et al.   NATURE BIOTECHNOLOGY

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

An Integrated Genetic and Cytogenetic Map of the Cucumber Genome

(2009) Yi Ren et al.   PLoS One

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

A space-efficient and accurate method for mapping and aligning cDNA sequences onto genomic sequence

(2008) Osamu Gotoh   NUCLEIC ACIDS RESEARCH