Extensive Horizontal Transfer and Homologous Recombination Generate Highly Chimeric Mitochondrial Genomes in Yeast

Comparison of mitochondrial genomes provides insights into intron dynamics and evolution in the caterpillar fungus Cordyceps militaris

(2015) Yongjie Zhang et al.   FUNGAL GENETICS AND BIOLOGY

Evolutionary Advantage Conferred by an Eukaryote-to-Eukaryote Gene Transfer Event in Wine Yeasts

(2015) Souhir Marsit et al.   MOLECULAR BIOLOGY AND EVOLUTION

DiscML: an R package for estimating evolutionary rates of discrete characters using maximum likelihood

(2014) Tane Kim et al.   BMC BIOINFORMATICS

A Genome-Wide Map of Mitochondrial DNA Recombination in Yeast

(2014) E. S. Fritsch et al.   GENETICS

Population Genomic Analysis Reveals Highly Conserved Mitochondrial Genomes in the Yeast Species Lachancea thermotolerans

(2014) Kelle C. Freel et al.   Genome Biology and Evolution

Population structure and reticulate evolution ofSaccharomyces eubayanusand its lager-brewing hybrids

(2014) David Peris et al.   MOLECULAR ECOLOGY

The 203 kbp Mitochondrial Genome of the Phytopathogenic Fungus Sclerotinia borealis Reveals Multiple Invasions of Introns and Genomic Duplications

(2014) Andrey V. Mardanov et al.   PLoS One

Massive programmed translational jumping in mitochondria

(2014) B. F. Lang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Horizontal Transfer and Gene Conversion as an Important Driving Force in Shaping the Landscape of Mitochondrial Introns

(2014) Baojun Wu et al.   G3-Genes Genomes Genetics

Consed: a graphical editor for next-generation sequencing

(2013) David Gordon et al.   BIOINFORMATICS

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria

(2013) Jiqiang Ling et al.   NUCLEIC ACIDS RESEARCH

Rapid Mitochondrial Genome Evolution through Invasion of Mobile Elements in Two Closely Related Species of Arbuscular Mycorrhizal Fungi

(2013) Denis Beaudet et al.   PLoS One

Horizontal Transfer of Entire Genomes via Mitochondrial Fusion in the Angiosperm Amborella

(2013) D. W. Rice et al.   SCIENCE

Mitochondrial Genome Evolution in a Single Protoploid Yeast Species

(2013) Paul P. Jung et al.   G3-Genes Genomes Genetics

Massive Mitochondrial Gene Transfer in a Parasitic Flowering Plant Clade

(2013) Zhenxiang Xi et al.   PLoS Genetics

Sequencing of mitochondrial genomes of nine Aspergillus and Penicillium species identifies mobile introns and accessory genes as main sources of genome size variability

(2012) Vinita Joardar et al.   BMC GENOMICS

Relationships among genera of theSaccharomycotina(Ascomycota) from multigene phylogenetic analysis of type species

(2012) Cletus P. Kurtzman et al.   FEMS YEAST RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Evolutionary Role of Interspecies Hybridization and Genetic Exchanges in Yeasts

(2012) Lucia Morales et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Group I Intron–Mediated Trans-splicing in Mitochondria of Gigaspora rosea and a Robust Phylogenetic Affiliation of Arbuscular Mycorrhizal Fungi with Mortierellales

(2012) Maryam Nadimi et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evidence for Compensatory Evolution of Ribosomal Proteins in Response to Rapid Divergence of Mitochondrial rRNA

(2012) F. S. Barreto et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative Mitochondrial Genomics within and among Yeast Species of the Lachancea Genus

(2012) Anne Friedrich et al.   PLoS One

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Toward almost closed genomes with GapFiller

(2012) Marten Boetzer et al.   GENOME BIOLOGY

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

The Fungi: 1, 2, 3 … 5.1 million species?

(2011) Meredith Blackwell   AMERICAN JOURNAL OF BOTANY

Mitochondrial genomes of yeasts of the Yarrowia clade

(2011) Claude Gaillardin et al.   FEMS YEAST RESEARCH

“Patchy-Tachy” Leads to False Positives for Recombination

(2011) Stephanie Sun et al.   MOLECULAR BIOLOGY AND EVOLUTION

An unusual tRNAThr derived from tRNAHis reassigns in yeast mitochondria the CUN codons to threonine

(2011) Dan Su et al.   NUCLEIC ACIDS RESEARCH

SATé-II: Very Fast and Accurate Simultaneous Estimation of Multiple Sequence Alignments and Phylogenetic Trees

(2011) Kevin Liu et al.   SYSTEMATIC BIOLOGY

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Scaffolding pre-assembled contigs using SSPACE

(2010) Marten Boetzer et al.   BIOINFORMATICS

OrgConv: detection of gene conversion using consensus sequences and its application in plant mitochondrial and chloroplast homologs

(2010) Weilong Hao   BMC BIOINFORMATICS

Diversity of sponge mitochondrial introns revealed by cox 1 sequences of Tetillidae

(2010) Amir Szitenberg et al.   BMC EVOLUTIONARY BIOLOGY

Saccharomyces paradoxus and Saccharomyces cerevisiae reside on oak trees in New Zealand: evidence for migration from Europe and interspecies hybrids

(2010) Hanyao Zhang et al.   FEMS YEAST RESEARCH

Inferring Bacterial Genome Flux While Considering Truncated Genes

(2010) Weilong Hao et al.   GENETICS

The Agaricus bisporus cox1 Gene: The Longest Mitochondrial Gene and the Largest Reservoir of Mitochondrial Group I Introns

(2010) Cyril Férandon et al.   PLoS One

Gorgeous mosaic of mitochondrial genes created by horizontal transfer and gene conversion

(2010) W. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Molecular Mechanisms Cause Reproductive Isolation between Three Yeast Species

(2010) Jui-Yu Chou et al.   PLOS BIOLOGY

Controlled mixed culture fermentation: a new perspective on the use of non-Saccharomyces  yeasts in winemaking

(2009) Maurizio Ciani et al.   FEMS YEAST RESEARCH

Polymorphisms in Multiple Genes Contribute to the Spontaneous Mitochondrial Genome Instability of Saccharomyces cerevisiae S288C Strains

(2009) L. N. Dimitrov et al.   GENETICS

Population Genomics of Intron Splicing in 38 Saccharomyces cerevisiae Genome Sequences

(2009) Daniel A. Skelly et al.   Genome Biology and Evolution

Eukaryote-to-eukaryote gene transfer events revealed by the genome sequence of the wine yeast Saccharomyces cerevisiae EC1118

(2009) M. Novo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fine-scale mergers of chloroplast and mitochondrial genes create functional, transcompartmentally chimeric mitochondrial genes

(2009) W. Hao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Natural Populations of Saccharomyces kudriavzevii in Portugal Are Associated with Oak Bark and Are Sympatric with S. cerevisiae and S. paradoxus

(2008) J. P. Sampaio et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Relaxation of yeast mitochondrial functions after whole-genome duplication

(2008) H. Jiang et al.   GENOME RESEARCH

Velvet: Algorithms for de novo short read assembly using de Bruijn graphs

(2008) D. R. Zerbino et al.   GENOME RESEARCH

Purifying selection of mtDNA and its implications for understanding evolution and mitochondrial disease

(2008) James Bruce Stewart et al.   NATURE REVIEWS GENETICS

Horizontal gene transfer in eukaryotic evolution

(2008) Patrick J. Keeling et al.   NATURE REVIEWS GENETICS