Comprehensive identification of mutations induced by heavy-ion beam irradiation in Arabidopsis thaliana

The Plant Journal : for Cell and Molecular Biology
Tomonari HiranoTomoko Abe

Abstract

Heavy-ion beams are widely used for mutation breeding and molecular biology. Although the mutagenic effects of heavy-ion beam irradiation have been characterized by sequence analysis of some restricted chromosomal regions or loci, there have been no evaluations at the whole-genome level or of the detailed genomic rearrangements in the mutant genomes. In this study, using array comparative genomic hybridization (array-CGH) and resequencing, we comprehensively characterized the mutations in Arabidopsis thaliana genomes irradiated with Ar or Fe ions. We subsequently used this information to investigate the mutagenic effects of the heavy-ion beams. Array-CGH demonstrated that the average number of deleted areas per genome were 1.9 and 3.7 following Ar-ion and Fe-ion irradiation, respectively, with deletion sizes ranging from 149 to 602,180 bp; 81% of the deletions were accompanied by genomic rearrangements. To provide a further detailed analysis, the genomes of the mutants induced by Ar-ion beam irradiation were resequenced, and total mutations, including base substitutions, duplications, in/dels, inversions, and translocations, were detected using three algorithms. All three resequenced mutants had genomic rearrangements. Of the 2...Continue Reading

References

Oct 1, 1996·The Plant Journal : for Cell and Molecular Biology·E BruggemannG Storz
May 24, 2000·Proceedings of the National Academy of Sciences of the United States of America·David O FergusonF W Alt
Dec 29, 2000·Nature·Arabidopsis Genome Initiative
Aug 2, 2003·Science·José M AlonsoJoseph R Ecker
Jan 12, 2005·Journal of Experimental Botany·Naoya ShikazonoAtsushi Tanaka
Sep 5, 2006·PLoS Computational Biology·Carene RizzonBrandon S Gaut
Jul 24, 2007·Nature Cell Biology·David M WeinstockMaria Jasin
Apr 17, 2008·Journal of Radiation Research·M Hada, Alexandros G Georgakilas
Aug 16, 2008·The Plant Journal : for Cell and Molecular Biology·Atsushi J NaganoIkuko Hara-Nishimura
Jan 8, 2009·Plant Physiology·Arjun KrishnanAndy Pereira
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jun 10, 2009·Bioinformatics·Heng Li1000 Genome Project Data Processing Subgroup
Aug 1, 2009·Nature Methods·Korbinian SchneebergerStig Uggerhø Andersen
Feb 16, 2010·Genes & Genetic Systems·Ryouhei MoritaMinoru Nishimura
Dec 28, 2010·Mutation Research·Evelyne Sage, Lynn Harrison
Jan 12, 2011·Nature Biotechnology·James T RobinsonJill P Mesirov
Apr 27, 2011·The Plant Journal : for Cell and Molecular Biology·Ryan S AustinDavid S Guttman
May 3, 2011·DNA Repair·Cyril CharbonnelCharles I White
Oct 27, 2011·Mutation Research·Yoshihiro HaseIssay Narumi
Nov 17, 2011·BMC Plant Biology·Yusuke KazamaTomoko Abe
Jan 24, 2012·Nature Biotechnology·Akira AbeRyohei Terauchi
Apr 9, 2013·Frontiers in Genetics·Anabelle Decottignies
Apr 12, 2013·The Plant Journal : for Cell and Molecular Biology·Cordelia BolleBernd Weisshaar
Aug 21, 2013·Trends in Plant Science·Ales PecinkaGiang T H Vu
Sep 13, 2013·Genes & Genetic Systems·Yusuke KazamaTomoko Abe
Sep 21, 2013·Annual Review of Genetics·Ludovic Deriano, David B Roth
Jan 28, 2014·Genomics·Julio Fernandez-BanetZhengyan Kan
Feb 4, 2014·The International Journal of Biochemistry & Cell Biology·Christophe Lavelle, Nicolas Foray
Mar 13, 2014·DNA Repair·Philippe FritPatrick Calsou
Mar 25, 2014·BMC Genomics·Eric J BelfieldNicholas P Harberd

Citations

Oct 12, 2018·International Journal of Radiation Biology·Liqiu MaShin Hatakeyama
Jul 28, 2016·Genes & Genetic Systems·Kotaro IshiiTomoko Abe
Jul 26, 2017·Letters in Applied Microbiology·W HuJ Chen
Apr 2, 2019·Frontiers in Plant Science·Lutz GrohmannThorben Sprink
Apr 11, 2020·Frontiers in Plant Science·Yoshihiro HaseYutaka Oono
Feb 25, 2021·Bioscience, Biotechnology, and Biochemistry·Kazuhide TsuneizumiTomoko Abe

Related Concepts

Argon
Genotoxic Stress
Iron
Ionizing Radiation
Gene Rearrangement
Arabidopsis thaliana <plant>
Sequence Determinations, DNA
DNA, Plant
Heavy Ions
Genomics

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Alzheimer's Disease: MS4A

Variants within the membrane-spanning 4-domains subfamily A (MS4A) gene cluster have recently been implicated in Alzheimer's disease in genome-wide association studies. Here is the latest research on Alzheimer's disease and MS4A.

Pediculosis pubis

Pediculosis pubis is a disease caused by a parasitic insect known as Pthirus pubis, which infests human pubic hair, as well as other areas with hair including eye lashes. Here is the latest research.

Rh Isoimmunization

Rh isoimmunization is a potentially preventable condition that occasionally is associated with significant perinatal morbidity or mortality. Discover the latest research on Rh Isoimmunization here.

Genetic Screens in iPSC-derived Brain Cells

Genetic screening is a critical tool that can be employed to define and understand gene function and interaction. This feed focuses on genetic screens conducted using induced pluripotent stem cell (iPSC)-derived brain cells. It also follows CRISPR-Cas9 approaches to generating genetic mutants as a means of understanding the effect of genetics on phenotype.

Enzyme Evolution

This feed focuses on molecular models of enzyme evolution and new approaches (such as adaptive laboratory evolution) to metabolic engineering of microorganisms. Here is the latest research.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Pharmacology of Proteinopathies

This feed focuses on the pharmacology of proteinopathies - diseases in which proteins abnormally aggregate (i.e. Alzheimer’s, Parkinson’s, etc.). Discover the latest research in this field with this feed.

Alignment-free Sequence Analysis Tools

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. Here is the latest research.