Comparison of nuclear, plastid, and mitochondrial phylogenies and the origin of wild octoploid strawberry species

Deep phylogenetic incongruence in the angiosperm clade Rosidae

(2015) Miao Sun et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenetic relationships, possible ancient hybridization, and biogeographic history of Abies (Pinaceae) based on data from nuclear, plastid, and mitochondrial genomes

(2015) Qiao-Ping Xiang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Fragaria : A genus with deep historical roots and ripe for evolutionary and ecological insights

(2014) Aaron Liston et al.   AMERICAN JOURNAL OF BOTANY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Genomic rearrangements and signatures of breeding in the allo-octoploid strawberry as revealed through an allele dose based SSR linkage map

(2014) Thijs van Dijk et al.   BMC PLANT BIOLOGY

Evolutionary Origins and Dynamics of Octoploid Strawberry Subgenomes Revealed by Dense Targeted Capture Linkage Maps

(2014) Jacob A. Tennessen et al.   Genome Biology and Evolution

On the adaptive value of cytoplasmic genomes in plants

(2014) Dan G. Bock et al.   MOLECULAR ECOLOGY

Mitochondrial DNA capture and divergence in Pinus provide new insights into the evolution of the genus

(2014) Baosheng Wang et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Incongruence among different mitochondrial regions: A case study using complete mitogenomes

(2014) Kelly A. Meiklejohn et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Homologous recombination and retention of a single form of most genes shape the highly chimeric mitochondrial genome of a cybrid plant

(2014) M. Virginia Sanchez-Puerta et al.   NEW PHYTOLOGIST

Whole Mitochondrial and Plastid Genome SNP Analysis of Nine Date Palm Cultivars Reveals Plastid Heteroplasmy and Close Phylogenetic Relationships among Cultivars

(2014) Jamal S. M. Sabir et al.   PLoS One

A Phylogenetic Analysis of the Genus Fragaria (Strawberry) Using Intron-Containing Sequence from the ADH-1 Gene

(2014) Laura M. DiMeglio et al.   PLoS One

Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics

(2014) Kevin Weitemier et al.   Applications in Plant Sciences

Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

(2013) Isabella Salamone et al.   AMERICAN JOURNAL OF BOTANY

Tuning a ménage à trois: Co-evolution and co-adaptation of nuclear and organellar genomes in plants

(2013) Stephan Greiner et al.   BIOESSAYS

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

(2013) H. Hirakawa et al.   DNA RESEARCH

A possible breakage of linkage disequilibrium between mitochondrial and chloroplast genomes during Emmer and Dinkel wheat evolution

(2013) Mai Tsujimura et al.   GENOME

Horizontal Transfer of DNA from the Mitochondrial to the Plastid Genome and Its Subsequent Evolution in Milkweeds (Apocynaceae)

(2013) Shannon C.K. Straub 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

Paternal leakage, heteroplasmy, and the evolution of plant mitochondrial genomes

(2013) David E. McCauley   NEW PHYTOLOGIST

Genome skimming reveals the origin of the Jerusalem Artichoke tuber crop species: neither from Jerusalem nor an artichoke

(2013) Dan G. Bock et al.   NEW PHYTOLOGIST

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

(2013) D. W. Rice et al.   SCIENCE

Targeted Sequence Capture Provides Insight into Genome Structure and Genetics of Male Sterility in a Gynodioecious Diploid Strawberry, Fragaria vesca ssp. bracteata (Rosaceae)

(2013) Jacob A. Tennessen et al.   G3-Genes Genomes Genetics

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

De novo assembly of the carrot mitochondrial genome using next generation sequencing of whole genomic DNA provides first evidence of DNA transfer into an angiosperm plastid genome

(2012) Massimo Iorizzo et al.   BMC PLANT BIOLOGY

An Evolutionary Network of Genes Present in the Eukaryote Common Ancestor Polls Genomes on Eukaryotic and Mitochondrial Origin

(2012) Thorsten Thiergart et al.   Genome Biology and Evolution

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria × ananassa subsp. cuneifolia

(2012) R Govindarajulu et al.   HEREDITY

Reconstruction of phylogenetic relationships in a highly reticulate group with deep coalescence and recent speciation (Hieracium, Asteraceae)

(2012) K Krak et al.   HEREDITY

Mitochondrial Gene Diversity Associated with the atp9 Stop Codon in Natural Populations of Wild Carrot (Daucus carota ssp. carota)

(2012) Jennifer R. Mandel et al.   JOURNAL OF HEREDITY

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

(2012) Wambui Njuguna et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Exceptional inheritance of plastids via pollen inNicotiana sylvestriswith no detectable paternal mitochondrial DNA in the progeny

(2012) Gregory Thyssen et al.   PLANT JOURNAL

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

The complex evolutionary dynamics of ancient and recent polyploidy in Leucaena (Leguminosae; Mimosoideae)

(2011) Rajanikanth Govindarajulu et al.   AMERICAN JOURNAL OF BOTANY

Navigating the tip of the genomic iceberg: Next-generation sequencing for plant systematics

(2011) Shannon C. K. Straub et al.   AMERICAN JOURNAL OF BOTANY

Functional characterization of gynodioecy in Fragaria vesca ssp. bracteata (Rosaceae)

(2011) Junmin Li et al.   ANNALS OF BOTANY

Building a model: developing genomic resources for common milkweed (Asclepias syriaca) with low coverage genome sequencing

(2011) Shannon CK Straub et al.   BMC GENOMICS

Male Sterility-Inducing Mitochondrial Genomes: How Do They Differ?

(2011) Tomohiko Kubo et al.   CRITICAL REVIEWS IN PLANT SCIENCES

A Reevaluation of Rice Mitochondrial Evolution Based on the Complete Sequence of Male-Fertile and Male-Sterile Mitochondrial Genomes

(2011) S. Bentolila et al.   PLANT PHYSIOLOGY

Nuclear and Chloroplast DNA Suggest a Complex Single Origin for the Threatened Allopolyploid Solidago houghtonii (Asteraceae) Involving Reticulate Evolution and Introgression

(2011) Pamela J. Laureto et al.   SYSTEMATIC BOTANY

Paternal Leakage and Heteroplasmy of Mitochondrial Genomes in Silene vulgaris: Evidence From Experimental Crosses

(2010) K. E. Bentley et al.   GENETICS

The genome of woodland strawberry (Fragaria vesca)

(2010) Vladimir Shulaev et al.   NATURE GENETICS

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

Discordant mtDNA and cpDNA phylogenies indicate geographic speciation and reticulation as driving factors for the diversification of the genus Picea

(2010) Marie Bouillé et al.   Tree Genetics & Genomes

Phylogenetic analysis of mitochondrial substitution rate variation in the angiosperm tribe Sileneae

(2009) Daniel B Sloan et al.   BMC EVOLUTIONARY BIOLOGY

Allopolyploidy in Fragariinae (Rosaceae): Comparing four DNA sequence regions, with comments on classification

(2009) Magnus Lundberg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): New insights from phylogenetic analyses of low-copy nuclear genes

(2009) M. Rousseau-Gueutin et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

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

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

Detection of rare paternal chloroplast inheritance in controlled crosses of the endangered sunflower Helianthus verticillatus

(2008) J R Ellis et al.   HEREDITY

Mitochondrial Heteroplasmy and Paternal Leakage in Natural Populations of Silene vulgaris, a Gynodioecious Plant

(2008) Stephanie A. Pearl et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY