Phylogenomic discovery of deleterious mutations facilitates hybrid potato breeding

Phylogenomic discordance suggests polytomies along the backbone of the large genus Solanum

(2022) Edeline Gagnon et al.   AMERICAN JOURNAL OF BOTANY

Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

(2022) Genevieve Hoopes et al.   Molecular Plant

Genetic load: genomic estimates and applications in non-model animals

(2022) Giorgio Bertorelle et al.   NATURE REVIEWS GENETICS

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

(2022) Hequan Sun et al.   NATURE GENETICS

A Solanum lycopersicoides reference genome facilitates insights into tomato specialized metabolism and immunity

(2022) Adrian F. Powell et al.   PLANT JOURNAL

A multiple alignment workflow shows the effect of repeat masking and parameter tuning on alignment in plants

(2022) Yaoyao Wu et al.   Plant Genome

Genome architecture and tetrasomic inheritance of autotetraploid potato

(2022) Zhigui Bao et al.   Molecular Plant

Graph pangenome captures missing heritability and empowers tomato breeding

(2022) Yao Zhou et al.   NATURE

Synonymous mutations in representative yeast genes are mostly strongly non-neutral

(2022) Xukang Shen et al.   NATURE

Genome evolution and diversity of wild and cultivated potatoes

(2022) Dié Tang et al.   NATURE

Vegetable biology and breeding in the genomics era

(2022) Hongbo Li et al.   Science China-Life Sciences

De novo genome assembly of Solanum sitiens reveals structural variation associated with drought and salinity tolerance

(2021) Corentin Molitor et al.   BIOINFORMATICS

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Inferring the Genetic Basis of Sex Determination from the Genome of a Dioecious Nightshade

(2021) Meng Wu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Improved genome assembly and pan‐genome provide key insights on eggplant domestication and breeding

(2021) L. Barchi et al.   PLANT JOURNAL

Genome design of hybrid potato

(2021) Chunzhi Zhang et al.   CELL

Conserved noncoding sequences provide insights into regulatory sequence and loss of gene expression in maize

(2021) Baoxing Song et al.   GENOME RESEARCH

Wolfberry genomes and the evolution of Lycium (Solanaceae)

(2021) You-Long Cao et al.   Communications Biology

The multi‐omics basis of potato heterosis

(2021) Dawei Li et al.   Journal of Integrative Plant Biology

The chromosome-based genome provides insights into the evolution in water spinach

(2021) Yuanyuan Hao et al.   SCIENTIA HORTICULTURAE

The Physalis floridana genome provides insights into the biochemical and morphological evolution of Physalis fruits

(2021) Jiangjie Lu et al.   Horticulture Research

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Solyntus, the New Highly Contiguous Reference Genome for Potato (Solanum tuberosum)

(2020) Natascha van Lieshout et al.   G3-Genes Genomes Genetics

A Collinearity-incorporating Homology Inference Strategy for Connecting Emerging Assemblies in Triticeae Tribe as a Pilot Practice in the Plant Pangenomic Era

(2020) Yongming Chen et al.   Molecular Plant

Haplotype-resolved genome analyses of a heterozygous diploid potato

(2020) Qian Zhou et al.   NATURE GENETICS

Construction of a chromosome-scale long-read reference genome assembly for potato

(2020) Gina M Pham et al.   GigaScience

Genome sequence of Jaltomata addresses rapid reproductive trait evolution and enhances comparative genomics in the hyper-diverse Solanaceae

(2019) Meng Wu et al.   Genome Biology and Evolution

The genetic basis of inbreeding depression in potato

(2019) Chunzhi Zhang et al.   NATURE GENETICS

A critical comparison of technologies for a plant genome sequencing project

(2019) Pirita Paajanen et al.   GigaScience

The new potato

(2019) Erik Stokstad   SCIENCE

Crossover Interference: Shedding Light on the Evolution of Recombination

(2019) Sarah P. Otto et al.   Annual Review of Genetics

Draft genome sequence of Solanum aethiopicum provides insights into disease resistance, drought tolerance, and the evolution of the genome

(2019) Bo Song et al.   GigaScience

The Fate of Deleterious Variants in a Barley Genomic Prediction Population

(2019) Thomas J. Y. Kono et al.   GENETICS

qgg: an R package for large-scale quantitative genetic analyses

(2019) Palle Duun Rohde et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Comparative transcriptomics and genomic patterns of discordance in Capsiceae (Solanaceae)

(2018) Daniel Spalink et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene expression drives the evolution of dominance

(2018) Christian D. Huber et al.   Nature Communications

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

Whole-Genome Duplication and Plant Macroevolution

(2018) James W. Clark et al.   TRENDS IN PLANT SCIENCE

On the Road to Breeding 4.0: Unraveling the Good, the Bad, and the Boring of Crop Quantitative Genomics

(2018) Jason G. Wallace et al.   Annual Review of Genetics

The impact of genome evolution on the allotetraploid Nicotiana rustica – an intriguing story of enhanced alkaloid production

(2018) N. Sierro et al.   BMC GENOMICS

Genome sequences of two diploid wild relatives of cultivated sweetpotato reveal targets for genetic improvement

(2018) Shan Wu et al.   Nature Communications

Genetic Costs of Domestication and Improvement

(2017) Brook T Moyers et al.   JOURNAL OF HEREDITY

Cassava haplotype map highlights fixation of deleterious mutations during clonal propagation

(2017) Punna Ramu et al.   NATURE GENETICS

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

(2017) Shuqing Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome diversity of tuber-bearingSolanumuncovers complex evolutionary history and targets of domestication in the cultivated potato

(2017) Michael A. Hardigan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Evolutionary genomics of grape (Vitis viniferassp.vinifera) domestication

(2017) Yongfeng Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Eocene lantern fruits from Gondwanan Patagonia and the early origins of Solanaceae

(2017) Peter Wilf et al.   SCIENCE

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

(2017) Olga Dudchenko et al.   SCIENCE

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

(2017) Jinliang Yang et al.   PLoS Genetics

North Andean origin and diversification of the largest ithomiine butterfly genus

(2017) Donna Lisa De-Silva et al.   Scientific Reports

Reinventing Potato as a Diploid Inbred Line–Based Crop

(2016) Shelley H. Jansky et al.   CROP SCIENCE

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

(2016) Stefan M. Edwards et al.   GENETICS

A Domain in the bHLH Transcription Factor DYT1 Is Critical for Anther Development

(2016) Kathleen L. Farquharson   PLANT CELL

Genome sequence and analysis of the Japanese morning glory Ipomoea nil

(2016) Atsushi Hoshino et al.   Nature Communications

Improving Genetic Gain with Genomic Selection in Autotetraploid Potato

(2016) Anthony T. Slater et al.   Plant Genome

Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation

(2016) James B. Pease et al.   PLOS BIOLOGY

Genomic Prediction for Quantitative Traits Is Improved by Mapping Variants to Gene Ontology Categories in Drosophila melanogaster

(2016) Stefan M. Edwards et al.   GENETICS

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

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

BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS: Table 1.

(2015) Katharina J. Hoff et al.   BIOINFORMATICS

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Estimating the mutation load in human genomes

(2015) Brenna M. Henn et al.   NATURE REVIEWS GENETICS

Split-alignment of genomes finds orthologies more accurately

(2015) Martin C Frith et al.   GENOME BIOLOGY

Systematics, Diversity, Genetics, and Evolution of Wild and Cultivated Potatoes

(2014) David M. Spooner et al.   BOTANICAL REVIEW

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

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

The genome of the stress-tolerant wild tomato species Solanum pennellii

(2014) Anthony Bolger et al.   NATURE GENETICS

Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species

(2014) Seungill Kim et al.   NATURE GENETICS

A phylogenetic framework for evolutionary study of the nightshades (Solanaceae): a dated 1000-tip tree

(2013) Tiina Särkinen et al.   BMC EVOLUTIONARY BIOLOGY

Gene duplication as a driver of plant morphogenetic evolution

(2013) Stefan A Rensing   CURRENT OPINION IN PLANT BIOLOGY

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Improving the analysis of low heritability complex traits for enhanced genetic gain in potato

(2013) Anthony T. Slater et al.   THEORETICAL AND APPLIED GENETICS

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

(2012) Pablo Cingolani et al.   FLY

Genomic Prediction in Animals and Plants: Simulation of Data, Validation, Reporting, and Benchmarking

(2012) H. D. Daetwyler et al.   GENETICS

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

(2012) Jon-Matthew Belton et al.   METHODS

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

An integrated map of genetic variation from 1,092 human genomes

(2012)   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang 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

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

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Crop genomics: advances and applications

(2011) Peter L. Morrell et al.   NATURE REVIEWS GENETICS

Towards F1 Hybrid Seed Potato Breeding

(2011) Pim Lindhout et al.   POTATO RESEARCH

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

(2010) A. McKenna et al.   GENOME RESEARCH

Identifying a High Fraction of the Human Genome to be under Selective Constraint Using GERP++

(2010) Eugene V. Davydov et al.   PLoS Computational Biology

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

The genetics of inbreeding depression

(2009) Deborah Charlesworth et al.   NATURE REVIEWS GENETICS

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE