In and out: Evolution of viral sequences in the mitochondrial genomes of legumes (Fabaceae)

Can Green Algal Plastid Genome Size Be Explained by DNA Repair Mechanisms?

(2020) David Roy Smith   Genome Biology and Evolution

Extensive shifts from cis to trans splicing of gymnosperm mitochondrial introns

(2020) Wenhu Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Exploration of Plastid Phylogenomic Conflict Yields New Insights into the Deep Relationships of Leguminosae

(2020) Rong Zhang et al.   SYSTEMATIC BIOLOGY

Comparative Mitogenome Analysis of the Genus Trifolium Reveals Independent Gene Fission of ccmFn and Intracellular Gene Transfers in Fabaceae

(2020) In-Su Choi et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Microhomologies are associated with tandem duplications and structural variation in plant mitochondrial genomes

(2020) Hanhan Xia et al.   Genome Biology and Evolution

Biological and molecular characterization of Chenopodium quinoa mitovirus 1 reveals a distinct sRNA response compared to cytoplasmic RNA viruses.

(2019) L. Nerva et al.   JOURNAL OF VIROLOGY

Plant organellar DNA polymerases repair double-stranded breaks by microhomology-mediated end-joining

(2019) Paola L García-Medel et al.   NUCLEIC ACIDS RESEARCH

Reconstruction of ancestral genome reveals chromosome evolution history for selected legume species

(2019) Longhui Ren et al.   NEW PHYTOLOGIST

Cercis: A Non-polyploid Genomic Relic Within the Generally Polyploid Legume Family

(2019) Jacob S. Stai et al.   Frontiers in Plant Science

Ancient Mitochondrial Gene Transfer between Fungi and the Orchids

(2019) Brandon T Sinn et al.   MOLECULAR BIOLOGY AND EVOLUTION

A reference genome for pea provides insight into legume genome evolution

(2019) Jonathan Kreplak et al.   NATURE GENETICS

Fluctuations in Fabaceae mitochondrial genome size and content are both ancient and recent

(2019) In-Su Choi et al.   BMC PLANT BIOLOGY

Large‐scale genomic sequence data resolve the deepest divergences in the legume phylogeny and support a near‐simultaneous evolutionary origin of all six subfamilies

(2019) Erik J. M. Koenen et al.   NEW PHYTOLOGIST

A functional twintron, ‘zombie’ twintrons and a hypermobile group II intron invading itself in plant mitochondria

(2019) Simon Zumkeller et al.   NUCLEIC ACIDS RESEARCH

Microhomology-mediated end joining: Good, bad and ugly

(2018) Ja-Hwan Seol et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS

Evidence for contemporary plant mitoviruses

(2018) Max L. Nibert et al.   VIROLOGY

New insights into Phakopsora pachyrhizi infection based on transcriptome analysis in planta

(2018) Michelle Pires Rincão et al.   GENETICS AND MOLECULAR BIOLOGY

PacBio-Based Mitochondrial Genome Assembly of Leucaena trichandra (Leguminosae) and an Intrageneric Assessment of Mitochondrial RNA Editing

(2018) Lynsey Kovar et al.   Genome Biology and Evolution

Assembly and comparative analysis of the complete mitochondrial genome sequence of Sophora japonica ‘JinhuaiJ2’

(2018) Yancai Shi et al.   PLoS One

Genome-scale transfer of mitochondrial DNA from legume hosts to the holoparasite Lophophytum mirabile (Balanophoraceae)

(2018) M. Virginia Sanchez-Puerta et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Structure of a Thermostable Group II Intron Reverse Transcriptase with Template-Primer and Its Functional and Evolutionary Implications

(2017) Jennifer L. Stamos et al.   MOLECULAR CELL

GeSeq – versatile and accurate annotation of organelle genomes

(2017) Michael Tillich et al.   NUCLEIC ACIDS RESEARCH

A new subfamily classification of the Leguminosae based on a taxonomically comprehensive phylogeny – The Legume Phylogeny Working Group (LPWG)

(2017) Nasim Azani et al.   TAXON

Protein-Coding Genes’ Retrocopies and Their Functions

(2017) Magdalena Regina Kubiak et al.   Viruses-Basel

LOCALIZER: subcellular localization prediction of both plant and effector proteins in the plant cell

(2017) Jana Sperschneider et al.   Scientific Reports

Bioinformatic analysis of Arabidopsis reverse transcriptases with a zinc-finger domain

(2016) Santiago Valentín Galván-Gordillo et al.   BIOLOGIA

LINEs between Species: Evolutionary Dynamics of LINE-1 Retrotransposons across the Eukaryotic Tree of Life

(2016) Atma M. Ivancevic et al.   Genome Biology and Evolution

GinkgoandWelwitschiaMitogenomes Reveal Extreme Contrasts in Gymnosperm Mitochondrial Evolution

(2016) Wenhu Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Complete mitochondrial genomes from the ferns Ophioglossum californicum and Psilotum nudum are highly repetitive with the largest organellar introns

(2016) Wenhu Guo et al.   NEW PHYTOLOGIST

Unparalleled replacement of native mitochondrial genes by foreign homologs in a holoparasitic plant

(2016) M. Virginia Sanchez-Puerta et al.   NEW PHYTOLOGIST

CDD/SPARCLE: functional classification of proteins via subfamily domain architectures

(2016) Aron Marchler-Bauer et al.   NUCLEIC ACIDS RESEARCH

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

(2016) Todd M. Lowe et al.   NUCLEIC ACIDS RESEARCH

Ancient Traces of Tailless Retropseudogenes in Therian Genomes

(2015) Angela Noll et al.   Genome Biology and Evolution

A 3′ Poly(A) Tract Is Required for LINE-1 Retrotransposition

(2015) Aurélien J. Doucet et al.   MOLECULAR CELL

A survey of transposable element classification systems – A call for a fundamental update to meet the challenge of their diversity and complexity

(2015) Benoît Piégu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Plastid genome sequences of legumes reveal parallel inversions and multiple losses ofrps16in papilionoids

(2015) Erika N. Schwarz et al.   Journal of Systematics and Evolution

Evolution of group II introns

(2015) Steven Zimmerly et al.   Mobile DNA

Widespread mitovirus sequences in plant genomes

(2015) Jeremy A. Bruenn et al.   PeerJ

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Genes and Junk in Plant Mitochondria—Repair Mechanisms and Selection

(2014) Alan C. Christensen   Genome Biology and Evolution

Multiple Polyploidy Events in the Early Radiation of Nodulating and Nonnodulating Legumes

(2014) Steven B. Cannon et al.   MOLECULAR BIOLOGY AND EVOLUTION

BoxPlotR: a web tool for generation of box plots

(2014) Michaela Spitzer et al.   NATURE METHODS

Evolutionary and biotechnology implications of plastid genome variation in the inverted-repeat-lacking clade of legumes

(2014) Jamal Sabir et al.   PLANT BIOTECHNOLOGY JOURNAL

Profiling of extensively diversified plant LINEs reveals distinct plant-specific subclades

(2014) Tony Heitkam et al.   PLANT JOURNAL

RNA metabolism in plant mitochondria

(2014) Kamel Hammani et al.   TRENDS IN PLANT SCIENCE

Group II intron splicing factors in plant mitochondria

(2014) Gregory G. Brown et al.   Frontiers in Plant Science

The “fossilized” mitochondrial genome of Liriodendron tulipifera: ancestral gene content and order, ancestral editing sites, and extraordinarily low mutation rate

(2013) Aaron O Richardson et al.   BMC BIOLOGY

Plant Mitochondrial Genome Evolution Can Be Explained by DNA Repair Mechanisms

(2013) Alan C. Christensen   Genome Biology and Evolution

Reconstructing the deep-branching relationships of the papilionoid legumes

(2013) D. Cardoso et al.   SOUTH AFRICAN JOURNAL OF BOTANY

Global legume diversity assessment: Concepts, key indicators, and strategies

(2013) Tetsukazu Yahara et al.   TAXON

Mitochondrial Genome Sequence of the Legume Vicia faba

(2013) Valentine Negruk   Frontiers in Plant Science

Revisiting the phylogeny of papilionoid legumes: New insights from comprehensively sampled early-branching lineages

(2012) Domingos Cardoso et al.   AMERICAN JOURNAL OF BOTANY

Parallel Relaxation of Stringent RNA Recognition in Plant and Mammalian L1 Retrotransposons

(2012) Kazuhiko Ohshima   MOLECULAR BIOLOGY AND EVOLUTION

jModelTest 2: more models, new heuristics and parallel computing

(2012) Diego Darriba et al.   NATURE METHODS

The mitochondrial genome of Malus domestica and the import-driven hypothesis of mitochondrial genome expansion in seed plants

(2012) Vadim V. Goremykin et al.   PLANT JOURNAL

Responses of the pea aphid transcriptome to infection by facultative symbionts

(2011) G. R. Burke et al.   INSECT MOLECULAR BIOLOGY

Insights into the Evolution of Mitochondrial Genome Size from Complete Sequences of Citrullus lanatus and Cucurbita pepo (Cucurbitaceae)

(2010) A. J. Alverson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Recombination and the maintenance of plant organelle genome stability

(2010) Alexandre Maréchal et al.   NEW PHYTOLOGIST

Different integration site structures between L1 protein-mediated retrotransposition in cis and retrotransposition in trans

(2010) Kenji K Kojima   Mobile DNA

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

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

Whirly proteins maintain plastid genome stability in Arabidopsis

(2009) A. Marechal et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Evidence That the Non-Homologous End-Joining Repair Pathway Is Involved in LINE Retrotransposition

(2009) Jun Suzuki et al.   PLoS Genetics

DNA Transfer from Organelles to the Nucleus: The Idiosyncratic Genetics of Endosymbiosis

(2008) Tatjana Kleine et al.   Annual Review of Plant Biology

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

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