Transposon Insertions, Structural Variations, and SNPs Contribute to the Evolution of the Melon Genome

Use of targeted SNP selection for an improved anchoring of the melon (Cucumis melo L.) scaffold genome assembly

(2015) Jason M Argyris et al.   BMC GENOMICS

Interspecific and intraspecific gene variability in a 1-Mb region containing the highest density of NBS-LRR genes found in the melon genome

(2015) Víctor M González et al.   BMC GENOMICS

Structural variations in plant genomes

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

Evolution of Centromeric Retrotransposons in Grasses

(2014) Anupma Sharma et al.   Genome Biology and Evolution

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Insights into the Maize Pan-Genome and Pan-Transcriptome

(2014) C. N. Hirsch et al.   PLANT CELL

Extensive amplification of the E2F transcription factor binding sites by transposons during evolution ofBrassicaspecies

(2014) Elizabeth Hénaff et al.   PLANT JOURNAL

Structural and functional partitioning of bread wheat chromosome 3B

(2014) F. Choulet et al.   SCIENCE

LUMPY: a probabilistic framework for structural variant discovery

(2014) Ryan M Layer et al.   GENOME BIOLOGY

The 3,000 rice genomes project

(2014)   GigaScience

A Bountiful Harvest: Genomic Insights into Crop Domestication Phenotypes

(2013) Kenneth M. Olsen et al.   Annual Review of Plant Biology

High presence/absence gene variability in defense-related gene clusters of Cucumis melo

(2013) Víctor M González et al.   BMC GENOMICS

Comparative Genomic Paleontology across Plant Kingdom Reveals the Dynamics of TE-Driven Genome Evolution

(2013) Moaine El Baidouri et al.   Genome Biology and Evolution

The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution

(2013) Ignazio Verde et al.   NATURE GENETICS

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

(2013) Jianjian Qi et al.   NATURE GENETICS

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

(2013) S. R. Eichten et al.   PLANT CELL

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

Frequent adaptation and the McDonald-Kreitman test

(2013) P. W. Messer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SNP genotyping in melons: genetic variation, population structure, and linkage disequilibrium

(2013) Cristina Esteras et al.   THEORETICAL AND APPLIED GENETICS

Improving fruit and wine: what does genomics have to offer?

(2013) Sean Myles   TRENDS IN GENETICS

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

Hidden genetic nature of epigenetic natural variation in plants

(2013) Ales Pecinka et al.   TRENDS IN PLANT SCIENCE

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

(2012) T. Rausch et al.   BIOINFORMATICS

The Drosophila melanogaster Genetic Reference Panel

(2012) Trudy F. C. Mackay et al.   NATURE

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Maize HapMap2 identifies extant variation from a genome in flux

(2012) Jer-Ming Chia et al.   NATURE GENETICS

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

(2012) Shaogui Guo et al.   NATURE GENETICS

How important are transposons for plant evolution?

(2012) Damon Lisch   NATURE REVIEWS GENETICS

Primer3—new capabilities and interfaces

(2012) Andreas Untergasser et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Characterization of Nonreference Transposons Reveals Evolutionary Propensities of Transposons in Soybean

(2012) Z. Tian et al.   PLANT CELL

Retrotransposons Control Fruit-Specific, Cold-Dependent Accumulation of Anthocyanins in Blood Oranges

(2012) E. Butelli et al.   PLANT CELL

Structural Variants in the Soybean Genome Localize to Clusters of Biotic Stress-Response Genes

(2012) L. K. McHale et al.   PLANT PHYSIOLOGY

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

Bridging the gap between genome analysis and precision breeding in potato

(2012) Christiane Gebhardt   TRENDS IN GENETICS

Natural Selection in Gene-Dense Regions Shapes the Genomic Pattern of Polymorphism in Wild and Domesticated Rice

(2011) J. M. Flowers et al.   MOLECULAR BIOLOGY AND EVOLUTION

Miniature Inverted-Repeat Transposable Elements (MITEs) Have Been Accumulated through Amplification Bursts and Play Important Roles in Gene Expression and Species Diversity in Oryza sativa

(2011) C. Lu et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Identification of a functional transposon insertion in the maize domestication gene tb1

(2011) Anthony Studer et al.   NATURE GENETICS

Genome structural variation discovery and genotyping

(2011) Can Alkan et al.   NATURE REVIEWS GENETICS

Weighing the evidence for adaptation at the molecular level

(2011) Justin C. Fay   TRENDS IN GENETICS

Genome sequence of the palaeopolyploid soybean

(2010) Jeremy Schmutz et al.   NATURE

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

Evolutionary conservation, diversity and specificity of LTR-retrotransposons in flowering plants: insights from genome-wide analysis and multi-specific comparison

(2010) Jianchang Du et al.   PLANT JOURNAL

Cucumber (Cucumis sativus) and melon (C. melo) have numerous wild relatives in Asia and Australia, and the sister species of melon is from Australia

(2010) P. Sebastian et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Food Security: The Challenge of Feeding 9 Billion People

(2010) H. C. J. Godfray et al.   SCIENCE

Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads

(2009) K. Ye et al.   BIOINFORMATICS

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

Frequency Spectrum Neutrality Tests: One for All and All for One

(2009) G. Achaz   GENETICS

Natural Selection on Synonymous and Nonsynonymous Mutations Shapes Patterns of Polymorphism in Populus tremula

(2009) P. K. Ingvarsson   MOLECULAR BIOLOGY AND EVOLUTION

The Sorghum bicolor genome and the diversification of grasses

(2009) Andrew H. Paterson et al.   NATURE

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

BreakDancer: an algorithm for high-resolution mapping of genomic structural variation

(2009) Ken Chen et al.   NATURE METHODS

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Maize Inbreds Exhibit High Levels of Copy Number Variation (CNV) and Presence/Absence Variation (PAV) in Genome Content

(2009) Nathan M. Springer et al.   PLoS Genetics

Pervasive Hitchhiking at Coding and Regulatory Sites in Humans

(2009) James J. Cai et al.   PLoS Genetics