Causes of Mutation Rate Variability in Plant Genomes

Mutation bias reflects natural selection in Arabidopsis thaliana

(2022) J. Grey Monroe et al.   NATURE

DNA Repair in Space and Time: Safeguarding the Genome with the Cohesin Complex

(2022) Jamie Phipps et al.   Genes

How Sequence Context-Dependent Mutability Drives Mutation Rate Variation in the Genome

(2022) Madeleine Oman et al.   Genome Biology and Evolution

Somatic mutation rates scale with lifespan across mammals

(2022) Alex Cagan et al.   NATURE

Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa

(2022) Xu Cai et al.   PLANT BIOTECHNOLOGY JOURNAL

Arabidopsis mediator subunit 17 connects transcription with DNA repair after UV‐B exposure

(2022) Marisol Giustozzi et al.   PLANT JOURNAL

The histone H3.1 variant regulates TONSOKU-mediated DNA repair during replication

(2022) Hossein Davarinejad et al.   SCIENCE

The Mutational, Epigenetic, and Transcriptional Effects Between Mixed High-Energy Particle Field (CR) and 7Li-Ion Beams (LR) Radiation in Wheat M1 Seedlings

(2022) Bo Li et al.   Frontiers in Plant Science

Graph pangenome captures missing heritability and empowers tomato breeding

(2022) Yao Zhou et al.   NATURE

Epigenetic features drastically impact CRISPR–Cas9 efficacy in plants

(2022) Trevor Weiss et al.   PLANT PHYSIOLOGY

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

The population genomics of adaptive loss of function

(2021) J. Grey Monroe et al.   HEREDITY

DNA damage—how and why we age?

(2021) Matt Yousefzadeh et al.   eLife

De novo mutation rate variation and its determinants in Chlamydomonas

(2021) Eugenio López-Cortegano et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice

(2021) Wei Yan et al.   Frontiers in Plant Science

The mutational landscape of human somatic and germline cells

(2021) Luiza Moore et al.   NATURE

Epigenetics: a catalyst of plant immunity against pathogens

(2021) Adam Hannan Parker et al.   NEW PHYTOLOGIST

Genomic impact of stress-induced transposable element mobility in Arabidopsis

(2021) David Roquis et al.   NUCLEIC ACIDS RESEARCH

A histone H3K4me1-specific binding protein is required for siRNA accumulation and DNA methylation at a subset of loci targeted by RNA-directed DNA methylation

(2021) Qingfeng Niu et al.   Nature Communications

Author Correction: PDX1LOW MAFALOW β-cells contribute to islet function and insulin release

(2021) Daniela Nasteska et al.   Nature Communications

The important contribution of transposable elements to phenotypic variation and evolution

(2021) Nathan S. Catlin et al.   CURRENT OPINION IN PLANT BIOLOGY

Mutation rate and spectrum in obligately outcrossing Caenorhabditis elegans mutation accumulation lines subjected to RNAi-induced knockdown of the mismatch repair gene msh-2

(2021) Vaishali Katju et al.   G3-Genes Genomes Genetics

Fast neutron mutagenesis in soybean enriches for small indels and creates frameshift mutations

(2021) Skylar R Wyant et al.   G3-Genes Genomes Genetics

Single‐nucleotide mosaicism in citrus: Estimations of somatic mutation rates and total number of variants

(2021) Estela Perez‐Roman et al.   Plant Genome

Tobacco smoking and somatic mutations in human bronchial epithelium

(2020) Kenichi Yoshida et al.   NATURE

H3K36me3, message from chromatin to DNA damage repair

(2020) Zhongxing Sun et al.   Cell and Bioscience

A phylogenomic approach reveals a low somatic mutation rate in a long-lived plant

(2020) Adam J. Orr et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Mutational signatures are jointly shaped by DNA damage and repair

(2020) Nadezda V. Volkova et al.   Nature Communications

Pan-Genome of Wild and Cultivated Soybeans

(2020) Yucheng Liu et al.   CELL

Evolution of mutation rate in astronomically large phytoplankton populations

(2020) Marc Krasovec et al.   Genome Biology and Evolution

MSH1is required for maintenance of the low mutation rates in plant mitochondrial and plastid genomes

(2020) Zhiqiang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimation of the SNP Mutation Rate in Two Vegetatively Propagating Species of Duckweed

(2020) George Sandler et al.   G3-Genes Genomes Genetics

Thermal stress accelerates Arabidopsis thaliana mutation rate

(2020) Eric J. Belfield et al.   GENOME RESEARCH

Plant stem-cell organization and differentiation at single-cell resolution

(2020) James W. Satterlee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The architecture of intra-organism mutation rate variation in plants

(2019) Long Wang et al.   PLOS BIOLOGY

First Estimation of the Spontaneous Mutation Rate in Diatoms

(2019) Marc Krasovec et al.   Genome Biology and Evolution

Transposition favors the generation of large effect mutations that may facilitate rapid adaption

(2019) Leandro Quadrana et al.   Nature Communications

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

DNA Base Excision Repair in Plants: An Unfolding Story With Familiar and Novel Characters

(2019) Teresa Roldán-Arjona et al.   Frontiers in Plant Science

PDS5 proteins are required for proper cohesin dynamics and participate in replication fork protection

(2019) Carmen Morales et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Mutation Rate and the Age of the Sex Chromosomes in Silene latifolia

(2018) Marc Krasovec et al.   CURRENT BIOLOGY

H3K36me3-mediated mismatch repair preferentially protects actively transcribed genes from mutation

(2018) Yaping Huang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns

(2018) Onur Oztas et al.   Nature Communications

Do plants have a segregated germline?

(2018) Robert Lanfear   PLOS BIOLOGY

Evolutionary determinants of genome-wide nucleotide composition

(2018) Hongan Long et al.   Nature Ecology & Evolution

Fine-Grained Analysis of Spontaneous Mutation Spectrum and Frequency in Arabidopsis thaliana

(2018) Mao-Lun Weng et al.   GENETICS

COSMIC: the Catalogue Of Somatic Mutations In Cancer

(2018) John G Tate et al.   NUCLEIC ACIDS RESEARCH

Ionizing radiation manifesting DNA damage response in plants: An overview of DNA damage signaling and repair mechanisms in plants

(2018) Jin-Hong Kim et al.   PLANT SCIENCE

DNA mismatch repair preferentially protects genes from mutation

(2017) Eric J. Belfield et al.   GENOME RESEARCH

Spontaneous Mutation Rate in the Smallest Photosynthetic Eukaryotes

(2017) Marc Krasovec et al.   MOLECULAR BIOLOGY AND EVOLUTION

Gene Targeting by Homology-Directed Repair in Rice Using a Geminivirus-Based CRISPR/Cas9 System

(2017) Mugui Wang et al.   Molecular Plant

Whole-genome landscapes of major melanoma subtypes

(2017) Nicholas K. Hayward et al.   NATURE

PCSD: a plant chromatin state database

(2017) Yue Liu et al.   NUCLEIC ACIDS RESEARCH

The Sequences of 1,504 Mutants in the Model Rice Variety Kitaake Facilitate Rapid Functional Genomic Studies

(2017) Guotian Li et al.   PLANT CELL

Contributions of Zea mays subspecies mexicana haplotypes to modern maize

(2017) Ning Yang et al.   Nature Communications

Genome-Wide Sequencing of 41 Rice ( Oryza sativa L.) Mutated Lines Reveals Diverse Mutations Induced by Fast-Neutron Irradiation

(2016) Guotian Li et al.   Molecular Plant

Genetic drift, selection and the evolution of the mutation rate

(2016) Michael Lynch et al.   NATURE REVIEWS GENETICS

Germline replications and somatic mutation accumulation are independent of vegetative life span inArabidopsis

(2016) J. Matthew Watson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UVR2 ensures transgenerational genome stability under simulated natural UV-B in Arabidopsis thaliana

(2016) Eva-Maria Willing et al.   Nature Communications

Principle and application of plant mutagenesis in crop improvement: a review

(2015) Yusuff Oladosu et al.   BIOTECHNOLOGY & BIOTECHNOLOGICAL EQUIPMENT

Extensive de novo mutation rate variation between individuals and across the genome ofChlamydomonas reinhardtii

(2015) Rob W. Ness et al.   GENOME RESEARCH

Parent–progeny sequencing indicates higher mutation rates in heterozygotes

(2015) Sihai Yang et al.   NATURE

DNA Damage and Repair in Plants under Ultraviolet and Ionizing Radiations

(2015) Sarvajeet S. Gill et al.   TheScientificWorldJOURNAL

Arabidopsis DNA polymerase lambda mutant is mildly sensitive to DNA double strand breaks but defective in integration of a transgene

(2015) Tomoyuki Furukawa et al.   Frontiers in Plant Science

DNA damage and repair in plants – from models to crops

(2015) Vasilissa Manova et al.   Frontiers in Plant Science

Involvement of the Cohesin Cofactor PDS5 (SPO76) During Meiosis and DNA Repair in Arabidopsis thaliana

(2015) Mónica Pradillo et al.   Frontiers in Plant Science

DNA Damage and Repair in Plants under Ultraviolet and Ionizing Radiations

(2015) Sarvajeet S. Gill et al.   Scientific World Journal

Human mediator MED17 subunit plays essential roles in gene regulation by associating with the transcription and DNA repair machineries

(2014) Yuko Kikuchi et al.   GENES TO CELLS

Environmentally responsive genome-wide accumulation of de novoArabidopsis thalianamutations and epimutations

(2014) Caifu Jiang et al.   GENOME RESEARCH

Chromatin structure and radiation-induced DNA damage: From structural biology to radiobiology

(2014) Christophe Lavelle et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

Insights into the Maize Pan-Genome and Pan-Transcriptome

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

Sequential switching of binding partners on PCNA during in vitro Okazaki fragment maturation

(2014) Daniel Dovrat et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Histone Mark H3K36me3 Regulates Human DNA Mismatch Repair through Its Interaction with MutSα

(2013) Feng Li et al.   CELL

Mediator links transcription and DNA repair by facilitating Rad2/XPG recruitment

(2013) F. Eyboulet et al.   GENES & DEVELOPMENT

No Gene-Specific Optimization of Mutation Rate in Escherichia coli

(2013) X. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions

(2013) Annabelle Haudry et al.   NATURE GENETICS

Sequence-dependent thymine dimer formation and photoreversal rates in double-stranded DNA

(2013) Yu Kay Law et al.   PHOTOCHEMICAL & PHOTOBIOLOGICAL SCIENCES

Synthetic nucleases for genome engineering in plants: prospects for a bright future

(2013) Holger Puchta et al.   PLANT JOURNAL

Poly(ADP-ribose)polymerases are involved in microhomology mediated back-up non-homologous end joining in Arabidopsis thaliana

(2013) Qi Jia et al.   PLANT MOLECULAR BIOLOGY

A SCARECROW-RETINOBLASTOMA Protein Network Controls Protective Quiescence in the Arabidopsis Root Stem Cell Organizer

(2013) Alfredo Cruz-Ramírez et al.   PLOS BIOLOGY

Non-random mutation: The evolution of targeted hypermutation and hypomutation

(2012) Iñigo Martincorena et al.   BIOESSAYS

Estimate of the Spontaneous Mutation Rate in Chlamydomonas reinhardtii

(2012) Rob W. Ness et al.   GENETICS

Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana

(2012) E. J. Belfield et al.   GENOME RESEARCH

Evidence of non-random mutation rates suggests an evolutionary risk management strategy

(2012) Iñigo Martincorena et al.   NATURE

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

(2012) E. Butelli et al.   PLANT CELL

Eukaryotic Class II Cyclobutane Pyrimidine Dimer Photolyase Structure Reveals Basis for Improved Ultraviolet Tolerance in Plants

(2011) Kenichi Hitomi et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Have a break: determinants of meiotic DNA double strand break (DSB) formation and processing in plants

(2011) B. Edlinger et al.   JOURNAL OF EXPERIMENTAL BOTANY

Abiotic stress leads to somatic and heritable changes in homologous recombination frequency, point mutation frequency and microsatellite stability in Arabidopsis plants

(2011) Youli Yao et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Variation in the mutation rate across mammalian genomes

(2011) Alan Hodgkinson et al.   NATURE REVIEWS GENETICS

Epigenetic Regulation of Repetitive Elements Is Attenuated by Prolonged Heat Stress inArabidopsis

(2010) Ales Pecinka et al.   PLANT CELL

Microsatellite Instability in Arabidopsis Increases with Plant Development

(2010) A. Golubov et al.   PLANT PHYSIOLOGY

A General Model of Codon Bias Due to GC Mutational Bias

(2010) Gareth A. Palidwor et al.   PLoS One

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Evolution of the mutation rate

(2010) Michael Lynch   TRENDS IN GENETICS

Stress-Induced Activation of Heterochromatic Transcription

(2010) Mireille Tittel-Elmer et al.   PLoS Genetics

Chemical biology of mutagenesis and DNA repair: cellular responses to DNA alkylation

(2009) N. Shrivastav et al.   CARCINOGENESIS

Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution

(2009) A. Stoltzfus et al.   JOURNAL OF HEREDITY

Genotoxic stress in plants: Shedding light on DNA damage, repair and DNA repair helicases

(2008) Narendra Tuteja et al.   MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH

Histone Acetylation and Chromatin Remodeling Are Required for UV-B-Dependent Transcriptional Activation of Regulated Genes in Maize

(2008) P. Casati et al.   PLANT CELL