Complete Sequence of a 641-kb Insertion of Mitochondrial DNA in the Arabidopsis thaliana Nuclear Genome

Mutation bias reflects natural selection in Arabidopsis thaliana

(2022) J. Grey Monroe et al.   NATURE

Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae)

(2022) In‐Su Choi et al.   PLANT JOURNAL

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

(2021) Haoyu Cheng et al.   NATURE METHODS

High-quality Arabidopsis thaliana Genome Assembly with Nanopore and HiFi Long Reads

(2021) Bo Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

The genetic and epigenetic landscape of the Arabidopsis centromeres

(2021) Matthew Naish et al.   SCIENCE

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning

(2021) Peng Ni et al.   Nature Communications

Weighted minimizer sampling improves long read mapping

(2020) Chirag Jain et al.   BIOINFORMATICS

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

Evidence for multi-copy Mega-NUMTs in the human genome

(2020) Sabine Lutz-Bonengel et al.   NUCLEIC ACIDS RESEARCH

A chromosome-level sequence assembly reveals the structure of the Arabidopsis thaliana Nd-1 genome and its gene set

(2019) Boas Pucker et al.   PLoS One

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Correction of Persistent Errors in Arabidopsis Reference Mitochondrial Genomes

(2018) Daniel B. Sloan et al.   PLANT CELL

Mosaic mitochondrial-plastid insertions into the nuclear genome show evidence of both non-homologous end joining and homologous recombination

(2018) Shir Portugez et al.   BMC EVOLUTIONARY BIOLOGY

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

(2018) Mao-Lun Weng et al.   GENETICS

Quantifying the Number of Independent Organelle DNA Insertions in Genome Evolution and Human Health

(2017) Einat Hazkani-Covo et al.   Genome Biology and Evolution

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

DNA methylation in higher plants: Past, present and future

(2011) Boris F. Vanyushin et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Double-strand break repair processes drive evolution of the mitochondrial genome in Arabidopsis

(2011) Jaime I Davila et al.   BMC BIOLOGY

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

The Scale of Population Structure in Arabidopsis thaliana

(2010) Alexander Platt et al.   PLoS Genetics

Molecular Poltergeists: Mitochondrial DNA Copies (numts) in Sequenced Nuclear Genomes

(2010) Einat Hazkani-Covo et al.   PLoS Genetics

Diversity of the Arabidopsis Mitochondrial Genome Occurs via Nuclear-Controlled Recombination Activity

(2009) Maria P. Arrieta-Montiel et al.   GENETICS

Relative rates of synonymous substitutions in the mitochondrial, chloroplast and nuclear genomes of seed plants

(2008) G DROUIN et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Heat Stress Enhances the Accumulation of Polyadenylated Mitochondrial Transcripts in Arabidopsis thaliana

(2008) Alessio Adamo et al.   PLoS One