Parental origin of the allotetraploid tobacco Nicotiana benthamiana

Genome and transcriptome characterization of the glycoengineered Nicotiana benthamiana line ΔXT/FT

(2019) Matteo Schiavinato et al.   BMC GENOMICS

SoS Notebook: an interactive multi-language data analysis environment

(2018) Bo Peng et al.   BIOINFORMATICS

The Rise and Rise of Nicotiana benthamiana: A Plant for All Reasons

(2018) Julia Bally et al.   Annual Review of Phytopathology

Effect of Hybridization on Somatic Mutations and Genomic Rearrangements in Plants

(2018) Tufail Bashir et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Time-calibrated phylogenetic trees establish a lag between polyploidisation and diversification in Nicotiana (Solanaceae)

(2017) James J. Clarkson et al.   PLANT SYSTEMATICS AND EVOLUTION

Wild tobacco genomes reveal the evolution of nicotine biosynthesis

(2017) Shuqing Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

ETE 3: Reconstruction, Analysis, and Visualization of Phylogenomic Data

(2016) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

Sequencing and characterization of leaf transcriptomes of six diploid Nicotiana species

(2016) Ni Long et al.   Journal of Biological Research-Thessaloniki

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Current status and prospects for the study of Nicotiana genomics, genetics, and nicotine biosynthesis genes

(2015) Xuewen Wang et al.   MOLECULAR GENETICS AND GENOMICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The tobacco genome sequence and its comparison with those of tomato and potato

(2014) Nicolas Sierro et al.   Nature Communications

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

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

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

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

RECONSTRUCTING THE COMPLEX EVOLUTIONARY ORIGIN OF WILD ALLOPOLYPLOID TOBACCOS (NICOTIANASECTIONSUAVEOLENTES)

(2012) Laura J. Kelly et al.   EVOLUTION

A Draft Genome Sequence of Nicotiana benthamiana to Enhance Molecular Plant-Microbe Biology Research

(2012) Aureliano Bombarely et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

Next Generation Sequencing Reveals Genome Downsizing in Allotetraploid Nicotiana tabacum, Predominantly through the Elimination of Paternally Derived Repetitive DNAs

(2011) S. Renny-Byfield et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Mobilization of retrotransposons in synthetic allotetraploid tobacco

(2010) M. Petit et al.   NEW PHYTOLOGIST

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

Nicotiana benthamiana as a Production Platform for Artemisinin Precursors

(2010) Teun W. J. M. van Herpen et al.   PLoS One

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Nuclear glutamine synthetase evolution in Nicotiana: Phylogenetics and the origins of allotetraploid and homoploid (diploid) hybrids

(2009) James J. Clarkson et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Ups and Downs of Genome Size Evolution in Polyploid Species of Nicotiana (Solanaceae)

(2008) I. J. Leitch et al.   ANNALS OF BOTANY