Genomic analyses of the Linum distyly supergene reveal convergent evolution at the molecular level

Comparative Genomics Elucidates the Origin of a Supergene Controlling Floral Heteromorphism

(2022) Giacomo Potente et al.   MOLECULAR BIOLOGY AND EVOLUTION

pixy : Unbiased estimation of nucleotide diversity and divergence in the presence of missing data

(2021) Katharine L Korunes et al.   Molecular Ecology Resources

Mutation load at a mimicry supergene sheds new light on the evolution of inversion polymorphisms

(2021) Paul Jay et al.   NATURE GENETICS

The genomic architecture and evolutionary fates of supergenes

(2021) Juanita Gutiérrez-Valencia et al.   Genome Biology and Evolution

Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C

(2021) Zev N. Kronenberg et al.   Nature Communications

Origin and diversification of flax and their relationship with heterostyly across the range

(2021) Enrique Maguilla et al.   JOURNAL OF BIOGEOGRAPHY

Female self-incompatibility type in heterostylous Primula is determined by the brassinosteroid-inactivating cytochrome P450 CYP734A50

(2021) Cuong Nguyen Huu et al.   CURRENT BIOLOGY

Pistil Mating Type and Morphology Are Mediated by the Brassinosteroid Inactivating Activity of the S-Locus Gene BAHD in Heterostylous Turnera Species

(2021) Courtney M. Matzke et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Lep-Anchor: automated construction of linkage map anchored haploid genomes

(2020) Pasi Rastas   BIOINFORMATICS

Molecular Evolutionary Genetics Analysis (MEGA) for macOS

(2020) Glen Stecher et al.   MOLECULAR BIOLOGY AND EVOLUTION

Supergene evolution via stepwise duplications and neofunctionalization of a floral-organ identity gene

(2020) Cuong Nguyen Huu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Gene Ontology resource: enriching a GOld mine

(2020) et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase in 2021

(2020) et al.   NUCLEIC ACIDS RESEARCH

ngsLD: evaluating linkage disequilibrium using genotype likelihoods

(2019) Emma A Fox et al.   BIOINFORMATICS

The long and short of the S ‐locus in Turnera (Passifloraceae)

(2019) Joel S Shore et al.   NEW PHYTOLOGIST

‘A most complex marriage arrangement’: recent advances on heterostyly and unresolved questions

(2019) Spencer C. H. Barrett   NEW PHYTOLOGIST

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

MEGA X: Molecular Evolutionary Genetics Analysis across Computing Platforms

(2018) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Style polymorphism in Linum (Linaceae): a case of Mediterranean parallel evolution?

(2018) J. Ruiz-Martín et al.   PLANT BIOLOGY

Multiple convergent supergene evolution events in mating-type chromosomes

(2018) Sara Branco et al.   Nature Communications

Heavy-tailed prior distributions for sequence count data: removing the noise and preserving large differences

(2018) Anqi Zhu et al.   BIOINFORMATICS

Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies

(2018) Michael J. Roach et al.   BMC BIOINFORMATICS

Primula vulgaris (primrose) genome assembly, annotation and gene expression, with comparative genomics on the heterostyly supergene

(2018) Jonathan M. Cocker et al.   Scientific Reports

A short story gets longer: recent insights into the molecular basis of heterostyly

(2017) Christian Kappel et al.   JOURNAL OF EXPERIMENTAL BOTANY

Sequencing the genomic regions flanking S-linked PvGLO sequences confirms the presence of two GLO loci, one of which lies adjacent to the style-length determinant gene CYP734A50

(2017) Benjamin A. Burrows et al.   Plant Reproduction

Assembly of the draft genome of buckwheat and its applications in identifying agronomically useful genes

(2016) Yasuo Yasui et al.   DNA RESEARCH

Sequencing wild and cultivated cassava and related species reveals extensive interspecific hybridization and genetic diversity

(2016) Jessen V Bredeson et al.   NATURE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

Presence versus absence of CYP734A50 underlies the style-length dimorphism in primroses

(2016) Cuong Nguyen Huu et al.   eLife

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Integration of genetic and physical maps of thePrimula vulgaris Slocus and localization by chromosomein situhybridization

(2015) Jinhong Li et al.   NEW PHYTOLOGIST

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

Genetic Control of Floral Morph and Petal Pigmentation in Linum grandiflorum Desf., a Heterostylous Flax

(2015) Koichiro Ushijima et al.   Horticulture Journal

Convergent Genetic Architecture Underlies Social Organization in Ants

(2014) Jessica Purcell et al.   CURRENT BIOLOGY

Supergenes and Complex Phenotypes

(2014) Tanja Schwander et al.   CURRENT BIOLOGY

Heterostyly promotes disassortative pollination and reduces sexual interference in Darwin's primroses: evidence from experimental studies

(2014) Barbara Keller et al.   FUNCTIONAL ECOLOGY

Supergenes and their role in evolution

(2014) M J Thompson et al.   HEREDITY

Rfam 12.0: updates to the RNA families database

(2014) Eric P. Nawrocki et al.   NUCLEIC ACIDS RESEARCH

Arabidopsis VASCULAR-RELATED UNKNOWN PROTEIN1 Regulates Xylem Development and Growth by a Conserved Mechanism That Modulates Hormone Signaling

(2014) E. Grienenberger et al.   PLANT PHYSIOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Infernal 1.1: 100-fold faster RNA homology searches

(2013) E. P. Nawrocki et al.   BIOINFORMATICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels

(2012) Marcel H. Schulz et al.   BIOINFORMATICS

HaploMerger: Reconstructing allelic relationships for polymorphic diploid genome assemblies

(2012) S. Huang et al.   GENOME RESEARCH

S-LOCUS EARLY FLOWERING 3 Is Exclusively Present in the Genomes of Short-Styled Buckwheat Plants that Exhibit Heteromorphic Self-Incompatibility

(2012) Yasuo Yasui et al.   PLoS One

Contrasted Patterns of Molecular Evolution in Dominant and Recessive Self-Incompatibility Haplotypes in Arabidopsis

(2012) Pauline M. Goubet et al.   PLoS Genetics

MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

(2011) Carson Holt et al.   BMC BIOINFORMATICS

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Isolation of the floral morph-related genes in heterostylous flax (Linum grandiflorum): the genetic polymorphism and the transcriptional and post-transcriptional regulations of the S locus

(2011) Koichiro Ushijima et al.   PLANT JOURNAL

UniProt Knowledgebase: a hub of integrated protein data

(2011) M. Magrane et al.   Database-The Journal of Biological Databases and Curation

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser

(2010) Ari Löytynoja et al.   BMC BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome

(2009) E. Lieberman-Aiden et al.   SCIENCE

The Phylogeny of Linum and Linaceae Subfamily Linoideae, with Implications for Their Systematics, Biogeography, and Evolution of Heterostyly

(2009) Joshua McDill et al.   SYSTEMATIC BOTANY

AmiGO: online access to ontology and annotation data

(2008) Seth Carbon et al.   BIOINFORMATICS

Using native and syntenically mapped cDNA alignments to improve de novo gene finding

(2008) Mario Stanke et al.   BIOINFORMATICS

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

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