Related references
Note: Only part of the references are listed.Approaching complete genomes, transcriptomes and epi-omes with accurate long-read sequencing
Sam Kovaka et al.
NATURE METHODS (2023)
Extensive sequence duplication in Arabidopsis revealed by pseudo-heterozygosity
Benjamin Jaegle et al.
GENOME BIOLOGY (2023)
Polycomb proteins control floral determinacy by H3K27me3-mediated repression of pluripotency genes in Arabidopsis thaliana
Ralf Muller-Xing et al.
JOURNAL OF EXPERIMENTAL BOTANY (2022)
Endosperm Evolution by Duplicated and Neofunctionalized Type I MADS-Box Transcription Factors
Yichun Qiu et al.
MOLECULAR BIOLOGY AND EVOLUTION (2022)
Green plant genomes: What we know in an era of rapidly expanding opportunities
W. John Kress et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2022)
Adaptive introgression: how polyploidy reshapes gene flow landscapes
Roswitha Schmickl et al.
NEW PHYTOLOGIST (2021)
The Dfam community resource of transposable element families, sequence models, and genome annotations
Jessica Storer et al.
MOBILE DNA (2021)
De Novo Mutation and Rapid Protein (Co-)evolution during Meiotic Adaptation in Arabidopsis arenosa
Magdalena Bohutinska et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
The genetic and epigenetic landscape of the Arabidopsis centromeres
Matthew Naish et al.
SCIENCE (2021)
The Diverse Roles of FLOWERING LOCUS C in Annual and Perennial Brassicaceae Species
Wim J. J. Soppe et al.
FRONTIERS IN PLANT SCIENCE (2021)
Towards complete and error-free genome assemblies of all vertebrate species
Arang Rhie et al.
NATURE (2021)
Extended haplotype-phasing of long-read de novo genome assemblies using Hi-C
Zev N. Kronenberg et al.
NATURE COMMUNICATIONS (2021)
BUSCO Update: Novel and Streamlined Workflows along with Broader and Deeper Phylogenetic Coverage for Scoring of Eukaryotic, Prokaryotic, and Viral Genomes
Mose Manni et al.
MOLECULAR BIOLOGY AND EVOLUTION (2021)
Gradual evolution of allopolyploidy in Arabidopsis suecica
Robin Burns et al.
NATURE ECOLOGY & EVOLUTION (2021)
Concerted genomic and epigenomic changes accompany stabilization of Arabidopsis allopolyploids
Xinyu Jiang et al.
NATURE ECOLOGY & EVOLUTION (2021)
BRAKER2: automatic eukaryotic genome annotation with GeneMark-EP plus and AUGUSTUS supported by a protein database
Tomas Bruna et al.
NAR GENOMICS AND BIOINFORMATICS (2021)
Genetic variation and temperature affects hybrid barriers during interspecific hybridization
Katrine N. Bjerkan et al.
PLANT JOURNAL (2020)
The Plant DNA C-values database (release 7.1): an updated online repository of plant genome size data for comparative studies
Jaume Pellicer et al.
NEW PHYTOLOGIST (2020)
Identifying and removing haplotypic duplication in primary genome assemblies
Dengfeng Guan et al.
BIOINFORMATICS (2020)
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
Bui Quang Minh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2020)
RepeatModeler2 for automated genomic discovery of transposable element families
Jullien M. Flynn et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2020)
GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes
T. Rhyker Ranallo-Benavidez et al.
NATURE COMMUNICATIONS (2020)
Formation and diversification of a paradigm biosynthetic gene cluster in plants
Zhenhua Liu et al.
NATURE COMMUNICATIONS (2020)
Merqury: reference-free quality, completeness, and phasing assessment for genome assemblies
Arang Rhie et al.
GENOME BIOLOGY (2020)
GetOrganelle: a fast and versatile toolkit for accurate de novo assembly of organelle genomes
Jian-Jun Jin et al.
GENOME BIOLOGY (2020)
RIdeogram: drawing SVG graphics to visualize and map genome-wide data on the idiograms
Zhaodong Hao et al.
PEERJ COMPUTER SCIENCE (2020)
Maternal small RNAs mediate spatial-temporal regulation of gene expression, imprinting, and seed development in Arabidopsis
Ryan C. Kirkbride et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2019)
Assembly of long, error-prone reads using repeat graphs
Mikhail Kolmogorov et al.
NATURE BIOTECHNOLOGY (2019)
Differential retention of transposable element-derived sequences in outcrossing Arabidopsis genomes
Sylvain Legrand et al.
MOBILE DNA (2019)
Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype
Daehwan Kim et al.
NATURE BIOTECHNOLOGY (2019)
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Jay Ghurye et al.
PLOS COMPUTATIONAL BIOLOGY (2019)
Interspecific introgression mediates adaptation to whole genome duplication
Sarah Marburger et al.
NATURE COMMUNICATIONS (2019)
The MADS-box transcription factor PHERES1 controls imprinting in the endosperm by binding to domesticated transposons
Rita A. Batista et al.
ELIFE (2019)
OrthoFinder: phylogenetic orthology inference for comparative genomics
David M. Emms et al.
GENOME BIOLOGY (2019)
RaGOO: fast and accurate reference-guided scaffolding of draft genomes
Michael Alonge et al.
GENOME BIOLOGY (2019)
SyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies
Manish Goel et al.
GENOME BIOLOGY (2019)
Assembly of allele-aware, chromosomal-scale autopolyploid genomes based on Hi-C data
Xingtan Zhang et al.
NATURE PLANTS (2019)
BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
Robert M. Waterhouse et al.
MOLECULAR BIOLOGY AND EVOLUTION (2018)
Minimap2: pairwise alignment for nucleotide sequences
Heng Li
BIOINFORMATICS (2018)
Overcoming the species hybridization barrier by ploidy manipulation in the genus Oryza
Kaoru Tonosaki et al.
PLANT JOURNAL (2018)
FERTILIZATION-INDEPENDENT SEED-Polycomb Repressive Complex 2 Plays a Dual Role in Regulating Type I MADS-Box Genes in Early Endosperm Development
Shanshan Zhang et al.
PLANT PHYSIOLOGY (2018)
A Survey of MIKC Type MADS-Box Genes in Non-seed Plants: Algae, Bryophytes, Lycophytes and Ferns
Gokilavani Thangavel et al.
FRONTIERS IN PLANT SCIENCE (2018)
Patterns of polymorphism and selection in the subgenomes of the allopolyploid Arabidopsis kamchatica
Timothy Paape et al.
NATURE COMMUNICATIONS (2018)
Purge Haplotigs: allelic contig reassignment for third-gen diploid genome assemblies
Michael J. Roach et al.
BMC BIOINFORMATICS (2018)
Genome assembly and annotation of Arabidopsis halleri, a model for heavy metal hyperaccumulation and evolutionary ecology
Roman V. Briskine et al.
MOLECULAR ECOLOGY RESOURCES (2017)
Centromere location in Arabidopsis is unaltered by extreme divergence in CENH3 protein sequence
Shamoni Maheshwari et al.
GENOME RESEARCH (2017)
Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
Sergey Koren et al.
GENOME RESEARCH (2017)
Genome Sequencing Reveals the Origin of the Allotetraploid Arabidopsis suecica
Polina Yu. Novikova et al.
MOLECULAR BIOLOGY AND EVOLUTION (2017)
Araport11: a complete reannotation of the Arabidopsis thaliana reference genome
Chia-Yi Cheng et al.
PLANT JOURNAL (2017)
Endosperm-based hybridization barriers explain the pattern of gene flow between Arabidopsis lyrata and Arabidopsis arenosa in Central Europe
Clement Lafon-Placette et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)
Standardized Method for High-throughput Sterilization of Arabidopsis Seeds
Benson E. Lindsey et al.
JOVE-JOURNAL OF VISUALIZED EXPERIMENTS (2017)
BRAKER1: Unsupervised RNA-Seq-Based Genome Annotation with GeneMark-ET and AUGUSTUS
Katharina J. Hoff et al.
BIOINFORMATICS (2016)
Assemblytics: a web analytics tool for the detection of variants from an assembly
Maria Nattestad et al.
BIOINFORMATICS (2016)
Genomic Imprinting in the Endosperm Is Systematically Perturbed in Abortive Hybrid Tomato Seeds
Ana M. Florez-Rueda et al.
MOLECULAR BIOLOGY AND EVOLUTION (2016)
Sequencing of the genus Arabidopsis identifies a complex history of nonbifurcating speciation and abundant trans-specific polymorphism
Polina Yu Novikova et al.
NATURE GENETICS (2016)
Phased diploid genome assembly with single-molecule real-time sequencing
Chen-Shan Chin et al.
NATURE METHODS (2016)
Borrowed alleles and convergence in serpentine adaptation
Brian J. Arnold et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)
Juicebox Provides a Visualization System for Hi-C Contact Maps with Unlimited Zoom
Neva C. Durand et al.
CELL SYSTEMS (2016)
Conserved imprinting associated with unique epigenetic signatures in the Arabidopsis genus
Maja Klosinska et al.
NATURE PLANTS (2016)
BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs
Felipe A. Simao et al.
BIOINFORMATICS (2015)
Improving the Annotation of Arabidopsis lyrata Using RNA-Seq Data
Vimal Rawat et al.
PLOS ONE (2015)
Non-reciprocal Interspecies Hybridization Barriers in the Capsella Genus Are Established in the Endosperm
Carolin A. Rebernig et al.
PLOS GENETICS (2015)
Perturbation of Parentally Biased Gene Expression during Interspecific Hybridization
Diana Burkart-Waco et al.
PLOS ONE (2015)
featureCounts: an efficient general purpose program for assigning sequence reads to genomic features
Yang Liao et al.
BIOINFORMATICS (2014)
LoRDEC: accurate and efficient long read error correction
Leena Salmela et al.
BIOINFORMATICS (2014)
Genome-wide quantification of homeolog expression ratio revealed nonstochastic gene regulation in synthetic allopolyploid Arabidopsis
Satoru Akama et al.
NUCLEIC ACIDS RESEARCH (2014)
miR824-Regulated AGAMOUS-LIKE16 Contributes to Flowering Time Repression in Arabidopsis
Jin-Yong Hu et al.
PLANT CELL (2014)
The BOY NAMED SUE Quantitative Trait Locus Confers Increased Meiotic Stability to an Adapted Natural Allopolyploid of Arabidopsis
Isabelle M. Henry et al.
PLANT CELL (2014)
Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement
Bruce J. Walker et al.
PLOS ONE (2014)
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Michael I. Love et al.
GENOME BIOLOGY (2014)
The MaSuRCA genome assembler
Aleksey V. Zimin et al.
BIOINFORMATICS (2013)
QUAST: quality assessment tool for genome assemblies
Alexey Gurevich et al.
BIOINFORMATICS (2013)
Meiotic Adaptation to Genome Duplication in Arabidopsis arenosa
Levi Yant et al.
CURRENT BIOLOGY (2013)
MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability
Kazutaka Katoh et al.
MOLECULAR BIOLOGY AND EVOLUTION (2013)
The Capsella rubella genome and the genomic consequences of rapid mating system evolution
Tanja Slotte et al.
NATURE GENETICS (2013)
Early Disruption of Maternal-Zygotic Interaction and Activation of Defense-Like Responses in Arabidopsis Interspecific Crosses
Diana Burkart-Waco et al.
PLANT CELL (2013)
Importance of Gene Duplication in the Evolution of Genomic Imprinting Revealed by Molecular Evolutionary Analysis of the Type I MADS-Box Gene Family in Arabidopsis Species
Takanori Yoshida et al.
PLOS ONE (2013)
SEPALLATA1/2-suppressedmature apples have lowethylene, high auxin and reduced transcription of ripening-related genes
Robert J. Schaffer et al.
AOB PLANTS (2013)
Endosperm cellularization defines an important developmental transition for embryo development
Elisabeth Hehenberger et al.
DEVELOPMENT (2012)
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
Yupeng Wang et al.
NUCLEIC ACIDS RESEARCH (2012)
Hybrid Incompatibility in Arabidopsis Is Determined by a Multiple-Locus Genetic Network
Diana Burkart-Waco et al.
PLANT PHYSIOLOGY (2012)
Mind the Gap: Upgrading Genomes with Pacific Biosciences RS Long-Read Sequencing Technology
Adam C. English et al.
PLOS ONE (2012)
Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae)
Marte H. Jorgensen et al.
BMC EVOLUTIONARY BIOLOGY (2011)
A SEPALLATA gene is involved in the development and ripening of strawberry (FragariaXananassa Duch.) fruit, a non-climacteric tissue
Graham B. Seymour et al.
JOURNAL OF EXPERIMENTAL BOTANY (2011)
Integrative genomics viewer
James T. Robinson et al.
NATURE BIOTECHNOLOGY (2011)
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change
Tina T. Hu et al.
NATURE GENETICS (2011)
The Sequence Read Archive
Rasko Leinonen et al.
NUCLEIC ACIDS RESEARCH (2011)
The Emerging Importance of Type I MADS Box Transcription Factors for Plant Reproduction
Simona Masiero et al.
PLANT CELL (2011)
Arabidopsis hybrid speciation processes
Roswitha Schmickl et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Polycomb group proteins are required to couple seed coat initiation to fertilization
Pawel Roszak et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2011)
Genome-Wide Transcript Profiling of Endosperm without Paternal Contribution Identifies Parent-of-Origin-Dependent Regulation of AGAMOUS-LIKE36
Reza Shirzadi et al.
PLOS GENETICS (2011)
An Atlas of Type I MADS Box Gene Expression during Female Gametophyte and Seed Development in Arabidopsis
Marian Bemer et al.
PLANT PHYSIOLOGY (2010)
FastTree 2-Approximately Maximum-Likelihood Trees for Large Alignments
Morgan N. Price et al.
PLOS ONE (2010)
A hitchhiker's guide to the MADS world of plants
Lydia Gramzow et al.
GENOME BIOLOGY (2010)
Fast and accurate short read alignment with Burrows-Wheeler transform
Heng Li et al.
BIOINFORMATICS (2009)
Dosage-Dependent Deregulation of an AGAMOUS-LIKE Gene Cluster Contributes to Interspecific Incompatibility
Harkamal Walia et al.
CURRENT BIOLOGY (2009)
The Dynamic Ups and Downs of Genome Size Evolution in Brassicaceae
Martin A. Lysak et al.
MOLECULAR BIOLOGY AND EVOLUTION (2009)
MIKC* MADS Domain Heterodimers Are Required for Pollen Maturation and Tube Growth in Arabidopsis
Benjamin J. Adamczyk et al.
PLANT PHYSIOLOGY (2009)
Target Genes of the MADS Transcription Factor SEPALLATA3: Integration of Developmental and Hormonal Pathways in the Arabidopsis Flower
Kerstin Kaufmann et al.
PLOS BIOLOGY (2009)
Imprinting of the Polycomb Group Gene MEDEA Serves as a Ploidy Sensor in Arabidopsis
Aleksandra Erilova et al.
PLOS GENETICS (2009)
Mechanism of PHERES1 imprinting in Arabidopsis
Grigory Makarevich et al.
JOURNAL OF CELL SCIENCE (2008)
FLC or not FLC: the other side of vernalization
Cristina Madeira Alexandre et al.
JOURNAL OF EXPERIMENTAL BOTANY (2008)
The MADS domain protein DIANA acts together with AGAMOUS-LIKE80 to specify the central cell in Arabidopsis ovules
Marian Bemer et al.
PLANT CELL (2008)
The AGL62 MADS domain protein regulates cellularization during endosperm development in Arabidopsis
Il-Ho Kang et al.
PLANT CELL (2008)
AGL23, a type I MADS-box gene that controls female gametophyte and embryo development in Arabidopsis
Monica Colombo et al.
PLANT JOURNAL (2008)
AGL61 interacts with AGL80 and is required for central cell development in Arabidopsis
Joshua G. Steffen et al.
PLANT PHYSIOLOGY (2008)
MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress
Rita Arora et al.
BMC GENOMICS (2007)
Patterns of DNA variation among three centromere satellite families in Arabidopsis halleri and A. lyrata
Akira Kawabe et al.
JOURNAL OF MOLECULAR EVOLUTION (2007)
Estimation of nuclear DNA content in plants using flow cytometry
Jaroslav Dolezel et al.
NATURE PROTOCOLS (2007)
MIKC* MADS-protein complexes bind motifs enriched in the proximal region of late pollen-specific Arabidopsis promoters
Wim Verelst et al.
PLANT PHYSIOLOGY (2007)
Ethylene-induced stomatal closure in Arabidopsis occurs via AtrbohF-mediated hydrogen peroxide synthesis
Radhika Desikan et al.
PLANT JOURNAL (2006)
Parent-dependent loss of gene silencing during interspecies hybridization
Caroline Josefsson et al.
CURRENT BIOLOGY (2006)
Polycomb-group proteins repress the floral activator AGL19 in the FLC-independent vernalization pathway
Nicole Schoenrock et al.
GENES & DEVELOPMENT (2006)
Mechanisms of chromosome number reduction in Arabidopsis thaliana and related Brassicaceae species
MA Lysak et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)
Engineering a software tool for gene structure prediction in higher organisms
G Gremme et al.
INFORMATION AND SOFTWARE TECHNOLOGY (2005)
Comprehensive interaction map of the Arabidopsis MADS box transcription factors
S de Folter et al.
PLANT CELL (2005)
Evolution of genome size in Brassicaceae
JS Johnston et al.
ANNALS OF BOTANY (2005)
Type I MADS-box genes have experienced faster birth-and-death evolution than type II MADS-box genes in angiosperms
J Nam et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2004)
Characterizing polyploidy in Arabidopsis lyrata using chromosome counts and flow cytometry
S Dart et al.
CANADIAN JOURNAL OF BOTANY-REVUE CANADIENNE DE BOTANIQUE (2004)
Molecular and phylogenetic analyses of the complete MADS-box transcription factor family in Arabidopsis:: New openings to the MADS world
L Parenicová et al.
PLANT CELL (2003)
The Polycomb-group protein MEDEA regulates seed development by controlling expression of the MADS-box gene PHERES1
C Köhler et al.
GENES & DEVELOPMENT (2003)
Analysis of the Arabidopsis MADS AFFECTING FLOWERING gene family:: MAF2 prevents vernalization by short periods of cold
OJ Ratcliffe et al.
PLANT CELL (2003)
Down-regulation of TM29, a tomato SEPALLATA homolog, causes parthenocarpic fruit development and floral reversion
C Ampomah-Dwamena et al.
PLANT PHYSIOLOGY (2002)
Two ancient classes of MIKC-type MADS-box genes are present in the moss Physcomitrella patens
K Henschel et al.
MOLECULAR BIOLOGY AND EVOLUTION (2002)
Conversion of leaves into petals in Arabidopsis
S Pelaz et al.
CURRENT BIOLOGY (2001)
Analysis of the genome sequence of the flowering plant Arabidopsis thaliana
S Kaul et al.
NATURE (2000)
Arabidopsis species hybrids in the study of species differences and evolution of amphiploidy in plants
ME Nasrallah et al.
PLANT PHYSIOLOGY (2000)
Phenotypic instability and rapid gene silencing in newly formed arabidopsis allotetraploids
L Comai et al.
PLANT CELL (2000)
Share Paper
