S ub P haser : a robust allopolyploid subgenome phasing method based on subgenome‐specific k ‐mers

TEsorter: an accurate and fast method to classify LTR-retrotransposons in plant genomes

(2022) Ren-Gang Zhang et al.   Horticulture Research

Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

(2021) John T. Lovell et al.   NATURE

High quality haplotype‐resolved genome assemblies of Populus tomentosa Carr., a stabilized interspecific hybrid species that is widespread in Asia

(2021) Xinmin An et al.   Molecular Ecology Resources

Chromosome-scale assembly and evolution of the tetraploid Salvia splendens (Lamiaceae) genome

(2021) Kai-Hua Jia et al.   Horticulture Research

Haplotype-resolved genome assembly and allele-specific gene expression in cultivated ginger

(2021) Shi-Ping Cheng et al.   Horticulture Research

Exceptional subgenome stability and functional divergence in the allotetraploid Ethiopian cereal teff

(2020) Robert VanBuren et al.   Nature Communications

The genome sequence of segmental allotetraploid peanut Arachis hypogaea

(2019) David J. Bertioli et al.   NATURE GENETICS

The genome of cultivated peanut provides insight into legume karyotypes, polyploid evolution and crop domestication

(2019) Weijian Zhuang et al.   NATURE GENETICS

PolyCRACKER, a robust method for the unsupervised partitioning of polyploid subgenomes by signatures of repetitive DNA evolution

(2019) Sean P. Gordon et al.   BMC GENOMICS

Revisiting the origin of octoploid strawberry

(2019) Aaron Liston et al.   NATURE GENETICS

Reply to: Revisiting the origin of octoploid strawberry

(2019) Patrick P. Edger et al.   NATURE GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

The transcriptional landscape of polyploid wheat

(2018) R. H. Ramírez-González et al.   SCIENCE

Polyploidy, the Nucleotype, and Novelty: The Impact of Genome Doubling on the Biology of the Cell

(2018) Jeff J. Doyle et al.   INTERNATIONAL JOURNAL OF PLANT SCIENCES

The genome of Chenopodium quinoa

(2017) David E. Jarvis et al.   NATURE

The evolutionary significance of polyploidy

(2017) Yves Van de Peer et al.   NATURE REVIEWS GENETICS

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

ggtree: anrpackage for visualization and annotation of phylogenetic trees with their covariates and other associated data

(2016) Guangchuang Yu et al.   Methods in Ecology and Evolution

LTR retrotransposons, handy hitchhikers of plant regulation and stress response

(2015) Marie-Angèle Grandbastien   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome

(2014) et al.   SCIENCE

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

A fast, lock-free approach for efficient parallel counting of occurrences of k-mers

(2011) Guillaume Marçais et al.   BIOINFORMATICS

Polyploidy and angiosperm diversification

(2009) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Genomic Plasticity and the Diversity of Polyploid Plants

(2008) A. R. Leitch et al.   SCIENCE

The diversity of retrotransposons and the properties of their reverse transcriptases

(2008) Thomas H. Eickbush et al.   VIRUS RESEARCH