Chromosome-level and haplotype-resolved genome provides insight into the tetraploid hybrid origin of patchouli

Chromosome-scale and haplotype-resolved genome assembly of a tetraploid potato cultivar

(2022) Hequan Sun et al.   NATURE GENETICS

Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp

(2021) Sarah Farhat et al.   BMC BIOLOGY

Volatile metabolic profiling and functional characterization of four terpene synthases reveal terpenoid diversity in different tissues of Chrysanthemum indicum L

(2021) Zhiyi Zhou et al.   PHYTOCHEMISTRY

U1 snRNP regulates cancer cell migration and invasion in vitro

(2020) Jung-Min Oh et al.   Nature Communications

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

The epigenetic regulation of centromeres and telomeres in plants and animals

(2020) Magdalena Achrem et al.   Comparative Cytogenetics

Asterid phylogenomics/phylotranscriptomics uncover morphological evolutionary histories and support phylogenetic placement for numerous whole genome duplications

(2020) Caifei Zhang et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Scientific Foundation of Chinese Herbal Medicine against COVID-19

(2020) Elaine Lai-Han Leung et al.   Engineering

Overexpression of SrDXS1 and SrKAH enhances steviol glycosides content in transgenic Stevia plants

(2019) Junshi Zheng et al.   BMC PLANT BIOLOGY

Systematic survey of plant LTR-retrotransposons elucidates phylogenetic relationships of their polyprotein domains and provides a reference for element classification

(2019) Pavel Neumann et al.   Mobile DNA

CPGAVAS2, an integrated plastome sequence annotator and analyzer

(2019) Linchun Shi et al.   NUCLEIC ACIDS RESEARCH

The plastid genome and its implications in barcoding specific-chemotypes of the medicinal herb Pogostemon cablin in China

(2019) Caiyun Zhang et al.   PLoS One

Molecular identification and expression of sesquiterpene pathway genes responsible for patchoulol biosynthesis and regulation in Pogostemon cablin

(2019) Yun Tang et al.   Botanical Studies

Hybridization and a loss of sex shape genome‐wide diversity and the origin of species in the evening primroses ( Oenothera , Onagraceae)

(2019) Jesse D. Hollister et al.   NEW PHYTOLOGIST

One thousand plant transcriptomes and the phylogenomics of green plants

(2019)   NATURE

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

Inhibition effects of patchouli alcohol against influenza a virus through targeting cellular PI3K/Akt and ERK/MAPK signaling pathways

(2019) Yunjia Yu et al.   Virology Journal

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Combining RNA-seq data and homology-based gene prediction for plants, animals and fungi

(2018) Jens Keilwagen et al.   BMC BIOINFORMATICS

The causes and consequences of subgenome dominance in hybrids and recent polyploids

(2018) Kevin A. Bird et al.   NEW PHYTOLOGIST

Development and Characterization of High-Throughput EST-Based SSR Markers for Pogostemon cablin Using Transcriptome Sequencing

(2018) Puyue Ouyang et al.   MOLECULES

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

The Pfam protein families database in 2019

(2018) Sara El-Gebali et al.   NUCLEIC ACIDS RESEARCH

Recursive Paleohexaploidization Shaped the Durian Genome

(2018) Jinpeng Wang et al.   PLANT PHYSIOLOGY

The essential oil of patchouli, Pogostemon cablin : A review

(2017) Teris A. van Beek et al.   FLAVOUR AND FRAGRANCE JOURNAL

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Diversity-generating retroelements: natural variation, classification and evolution inferred from a large-scale genomic survey

(2017) Li Wu et al.   NUCLEIC ACIDS RESEARCH

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

In vitro induction and morphological characteristics of octoploid plants in Pogostemon cablin

(2016) Han-Jing Yan et al.   BREEDING SCIENCE

Patchouli (Pogostemon cablin Benth.): Botany, agrotechnology and biotechnological aspects

(2016) Mallappa Kumara Swamy et al.   INDUSTRIAL CROPS AND PRODUCTS

Phylogenetic relationships, character evolution and biogeographic diversification of Pogostemon s.l. (Lamiaceae)

(2016) Gang Yao et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome evolution in the allotetraploid frog Xenopus laevis

(2016) Adam M. Session et al.   NATURE

In vitro induction and characterization of tetraploid Patchouli (Pogostemon cablin Benth.) plant

(2016) Wahyu Widoretno   PLANT CELL TISSUE AND ORGAN CULTURE

A genetic delineation of Patchouli (Pogostemon cablin) revealed by specific-locus amplified fragment sequencing

(2016) Hui-Run Huang et al.   Journal of Systematics and Evolution

Survey of the genome of Pogostemon cablin provides insights into its evolutionary history and sesquiterpenoid biosynthesis

(2016) Yang He et al.   Scientific Reports

SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation

(2016) Wei Shen et al.   PLoS One

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

A Comprehensive Review on the Phytochemical Constituents and Pharmacological Activities of Pogostemon cablin Benth.: An Aromatic Medicinal Plant of Industrial Importance

(2015) Mallappa Swamy et al.   MOLECULES

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Atypical centromeres in plants—what they can tell us

(2015) Maria Cuacos et al.   Frontiers in Plant Science

Nonadditive Gene Expression in Polyploids

(2014) Mi-Jeong Yoo et al.   Annual Review of Genetics

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

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

Expression, purification and activity assay of a patchoulol synthase cDNA variant fused to thioredoxin in Escherichia coli

(2014) S. Hartwig et al.   PROTEIN EXPRESSION AND PURIFICATION

Two Evolutionarily Distinct Classes of Paleopolyploidy

(2013) Olivier Garsmeur et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

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

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Extensive chromosomal variation in a recently formed natural allopolyploid species, Tragopogon miscellus (Asteraceae)

(2012) M. Chester et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2011) Guillaume Marçais et al.   BIOINFORMATICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

(2011) J. C. Schnable et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Homoeologous shuffling and chromosome compensation maintain genome balance in resynthesized allopolyploid Brassica napus

(2011) Z. Xiong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences

(2010) Y. Han et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Infernal 1.0: inference of RNA alignments

(2009) E. P. Nawrocki et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(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

Evolutionary Genetics of Genome Merger and Doubling in Plants

(2008) Jeff J. Doyle et al.   Annual Review of Genetics

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

(2008) David Ellinghaus et al.   BMC BIOINFORMATICS

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY