A telomere-to-telomere gap-free reference genome of watermelon and its mutation library provide important resources for gene discovery and breeding

Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

(2022) Ann M. Mc Cartney et al.   NATURE METHODS

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

(2021) Haoyu Cheng et al.   NATURE METHODS

Copy Number Variation and Rearrangements Assessment in Cancer: Comparison of Droplet Digital PCR with the Current Approaches

(2021) Vincenza Ylenia Cusenza et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Development of a Duplex Digital PCR Method to Quantify Five Genetically Modified Soybean Events

(2021) Likun Long et al.   Food Analytical Methods

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

Gapless indica rice genome reveals synergistic contributions of active transposable elements and segmental duplications to rice genome evolution

(2021) Kui Li et al.   Molecular Plant

Two gap-free reference genomes and a global view of the centromere architecture in rice

(2021) Jia-Ming Song et al.   Molecular Plant

Genome assembly of the Chinese maize elite inbred line RP125 and its EMS mutant collection provide new resources for maize genetics research and crop improvement

(2021) Shujun Nie et al.   PLANT JOURNAL

A chromosome-level genome of a Kordofan melon illuminates the origin of domesticated watermelons

(2021) Susanne S. Renner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

(2021) Caroline Belser et al.   Communications Biology

AnchorWave: Sensitive alignment of genomes with high sequence diversity, extensive structural polymorphism, and whole-genome duplication

(2021) Baoxing Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The genetic and epigenetic landscape of the Arabidopsis centromeres

(2021) Matthew Naish et al.   SCIENCE

Markers for selection of three alleles of ClSUN25-26-27a (Cla011257) associated with fruit shape in watermelon

(2020) Reeve Legendre et al.   MOLECULAR BREEDING

Mapping-by-Sequencing via MutMap Identifies a Mutation in ZmCLE7 Underlying Fasciation in a Newly Developed EMS Mutant Population in an Elite Tropical Maize Inbred

(2020) Quan Hong Tran et al.   Genes

RepeatModeler2 for automated genomic discovery of transposable element families

(2020) Jullien M. Flynn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development and screening of EMS mutants with altered seed oil content or fatty acid composition in Brassica napus

(2020) Shan Tang et al.   PLANT JOURNAL

Molecular regulation ofZmMs7required for maize male fertility and development of a dominant male-sterility system in multiple species

(2020) Xueli An et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Generation and Characterization of a Foxtail Millet (Setaria italica) Mutant Library

(2019) Jing Sun et al.   Frontiers in Plant Science

Watermelon as a potential fruit snack

(2019) Makaepea M. Maoto et al.   INTERNATIONAL JOURNAL OF FOOD PROPERTIES

Genome of ‘Charleston Gray’, the principal American watermelon cultivar, and genetic characterization of 1,365 accessions in the U.S. National Plant Germplasm System watermelon collection

(2019) Shan Wu et al.   PLANT BIOTECHNOLOGY JOURNAL

The Second Site Modifier, Sympathy for the ligule, Encodes a Homolog of Arabidopsis ENHANCED DISEASE RESISTANCE4 and Rescues the Liguleless narrow Maize Mutant

(2019) Alyssa Anderson et al.   PLANT CELL

Combining next‐generation sequencing and progeny testing for rapid identification of induced recessive and dominant mutations in maize M 2 individuals

(2019) Marc C. Heuermann et al.   PLANT JOURNAL

A chromosome-scale genome assembly of cucumber (Cucumis sativus L.)

(2019) Qing Li et al.   GigaScience

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

(2019) Shaogui Guo et al.   NATURE GENETICS

Ethylene‐responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon

(2019) Nanqiao Liao et al.   PLANT BIOTECHNOLOGY JOURNAL

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Gene-Indexed Mutations in Maize

(2018) Xiaoduo Lu et al.   Molecular Plant

Genetic mapping reveals a candidate gene (ClFS1) for fruit shape in watermelon (Citrullus lanatus L.)

(2018) Junling Dou et al.   THEORETICAL AND APPLIED GENETICS

An EMS mutant library for cucumber

(2018) Chen CHEN et al.   Journal of Integrative Agriculture

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Phenomic and Genomic Characterization of a Mutant Platform in Cucurbita pepo

(2018) Alicia García et al.   Frontiers in Plant Science

Whole Genome Characterization of a Few EMS-Induced Mutants of Upland Rice Variety Nagina 22 Reveals a Staggeringly High Frequency of SNPs Which Show High Phenotypic Plasticity Towards the Wild-Type

(2018) Amitha M. V. Sevanthi et al.   Frontiers in Plant Science

Arabidopsis HSP70‐16 is required for flower opening under normal or mild heat stress temperatures

(2018) Xu Chen et al.   PLANT CELL AND ENVIRONMENT

Genetic Diversity in the Desert Watermelon Citrullus colocynthis and its Relationship with Citrullus Species as Determined by High-frequency Oligonucleotides-targeting Active Gene Markers

(2017) Amnon Levi et al.   JOURNAL OF THE AMERICAN SOCIETY FOR HORTICULTURAL SCIENCE

A single point mutation in Ms44 results in dominant male sterility and improves nitrogen use efficiency in maize

(2017) Tim Fox et al.   PLANT BIOTECHNOLOGY JOURNAL

A Tonoplast Sugar Transporter Underlies a Sugar Accumulation QTL in Watermelon

(2017) Yi Ren et al.   PLANT PHYSIOLOGY

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Genome-wide survey of artificial mutations induced by ethyl methanesulfonate and gamma rays in tomato

(2015) Kenta Shirasawa et al.   PLANT BIOTECHNOLOGY JOURNAL

Structural variations in plant genomes

(2014) R. K. Saxena et al.   Briefings in Functional Genomics

Natural Variation at sympathy for the ligule Controls Penetrance of the Semidominant Liguleless narrow-R Mutation in Zea mays

(2014) Elizabeth M. Buescher et al.   G3-Genes Genomes Genetics

Genetic and chemical characterization of an EMS induced mutation in Cucumis melo CRTISO gene

(2013) Navot Galpaz et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

Chromosome-scale scaffolding of de novo genome assemblies based on chromatin interactions

(2013) Joshua N Burton et al.   NATURE BIOTECHNOLOGY

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

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

(2012) Pablo Cingolani et al.   FLY

The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions

(2012) Shaogui Guo et al.   NATURE GENETICS

The genome of melon (Cucumis melo L.)

(2012) J. Garcia-Mas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Infernal 1.0: inference of RNA alignments

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

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY