Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops

Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

(2022) Yanting Shen et al.   Nature Communications

A high-quality genome assembly highlights rye genomic characteristics and agronomically important genes

(2021) Guangwei Li et al.   NATURE GENETICS

A chromosome-level Camptotheca acuminata genome assembly provides insights into the evolutionary origin of camptothecin biosynthesis

(2021) Minghui Kang et al.   Nature Communications

Insights from the first genome assembly of Onion (Allium cepa)

(2021) Richard Finkers et al.   G3-Genes Genomes Genetics

The Chinese pine genome and methylome unveil key features of conifer evolution

(2021) Shihui Niu et al.   CELL

Interspecific hybridization in Allium crops: status and prospectus

(2021) Ashwini Prashant Benke et al.   GENETIC RESOURCES AND CROP EVOLUTION

Identifying and removing haplotypic duplication in primary genome assemblies

(2020) Dengfeng Guan et al.   BIOINFORMATICS

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

Variability in S-Alk(en)yl-l-Cysteine Sulfoxides in Garlic within a Seven-Month Period Determined by a Liquid Chromatography – Tandem Mass Spectrometry Method

(2020) Michaela Rektorisova et al.   PLANT FOODS FOR HUMAN NUTRITION

Chromosome-level genome assembly, annotation and evolutionary analysis of the ornamental plant Asparagus setaceus

(2020) Shu-Fen Li et al.   Horticulture Research

Thiosulfinate Tolerance Is a Virulence Strategy of an Atypical Bacterial Pathogen of Onion

(2020) Shaun P. Stice et al.   CURRENT BIOLOGY

Gene and genome duplications in the evolution of chemodiversity: perspectives from studies of Lamiaceae

(2020) Benjamin R Lichman et al.   CURRENT OPINION IN PLANT BIOLOGY

A chromosome-level genome assembly of garlic (Allium sativum L.) provides insights into genome evolution and allicin biosynthesis

(2020) Xiudong Sun et al.   Molecular Plant

S-Alk(en)ylcysteine sulfoxides in the genus Allium: proposed biosynthesis, chemical conversion, and bioactivities

(2019) Naoko Yoshimoto et al.   JOURNAL OF EXPERIMENTAL BOTANY

Polyploidy promotes species diversification of Allium through ecological shifts

(2019) Ting‐Shen Han et al.   NEW PHYTOLOGIST

Resequencing of 414 cultivated and wild watermelon accessions identifies selection for fruit quality traits

(2019) Shaogui Guo et al.   NATURE GENETICS

Dissecting the Stereocontrolled Conversion of Short-Lived Sulfenic Acid by Lachrymatory Factor Synthase

(2019) Takatoshi Arakawa et al.   ACS Catalysis

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

LTR-retrotransposons in plants: Engines of evolution

(2017) Leonardo Galindo-González et al.   GENE

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

(2017) Sergey Koren et al.   GENOME RESEARCH

The Apostasia genome and the evolution of orchids

(2017) Guo-Qiang Zhang et al.   NATURE

The asparagus genome sheds light on the origin and evolution of a young Y chromosome

(2017) Alex Harkess et al.   Nature Communications

Physiological response and sulfur metabolism of the V. dahliae-infected tomato plants in tomato/potato onion companion cropping

(2016) Xuepeng Fu et al.   Scientific Reports

The Genome of Dendrobium officinale Illuminates the Biology of the Important Traditional Chinese Orchid Herb

(2015) Liang Yan et al.   Molecular Plant

The pineapple genome and the evolution of CAM photosynthesis

(2015) Ray Ming et al.   NATURE GENETICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Glucosinolate metabolism, functionality and breeding for the improvement of Brassicaceae vegetables

(2014) Masahiko Ishida et al.   BREEDING SCIENCE

The genome sequence of the orchid Phalaenopsis equestris

(2014) Jing Cai et al.   NATURE GENETICS

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

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

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome sequence of the date palm Phoenix dactylifera L

(2013) Ibrahim S. Al-Mssallem et al.   Nature Communications

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly

(2012) Ernest T Lam et al.   NATURE BIOTECHNOLOGY

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China

(2010) Q.-Q. Li et al.   ANNALS OF BOTANY

Population differentiation as a test for selective sweeps

(2010) H. Chen et al.   GENOME RESEARCH

Biosynthesis of glucosinolates – gene discovery and beyond

(2010) Ida E. Sønderby et al.   TRENDS IN PLANT SCIENCE

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Fine-grained annotation and classification of de novo predicted LTR retrotransposons

(2009) Sascha Steinbiss et al.   NUCLEIC ACIDS RESEARCH

Silencing Onion Lachrymatory Factor Synthase Causes a Significant Change in the Sulfur Secondary Metabolite Profile

(2008) C. C. Eady et al.   PLANT PHYSIOLOGY

A Retrotransposon-Mediated Gene Duplication Underlies Morphological Variation of Tomato Fruit

(2008) H. Xiao et al.   SCIENCE

Synteny and Collinearity in Plant Genomes

(2008) H. Tang et al.   SCIENCE

Construction of SSR-based chromosome map in bunching onion (Allium fistulosum)

(2008) Hikaru Tsukazaki et al.   THEORETICAL AND APPLIED GENETICS