Morphological dissection and cellular and transcriptome characterizations of bamboo pith cavity formation reveal a pivotal role of genes related to programmed cell death

BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics

(2017) Robert M Waterhouse et al.   MOLECULAR BIOLOGY AND EVOLUTION

The association of hormone signalling genes, transcription and changes in shoot anatomy during moso bamboo growth

(2017) Long Li et al.   PLANT BIOTECHNOLOGY JOURNAL

An NADPH Oxidase RBOH Functions in Rice Roots during Lysigenous Aerenchyma Formation under Oxygen-Deficient Conditions

(2017) Takaki Yamauchi et al.   PLANT CELL

Regulation of Root Traits for Internal Aeration and Tolerance to Soil Waterlogging-Flooding Stress

(2017) Takaki Yamauchi et al.   PLANT PHYSIOLOGY

An Efficient Plant Regeneration and Transformation System of Ma Bamboo (Dendrocalamus latiflorus Munro) Started from Young Shoot as Explant

(2017) Shanwen Ye et al.   Frontiers in Plant Science

Exploring key cellular processes and candidate genes regulating the primary thickening growth of Moso underground shoots

(2016) Qiang Wei et al.   NEW PHYTOLOGIST

A lysigenic programmed cell death-dependent process shapes schizogenously formed aerenchyma in the stems of the waterweedEgeria densa

(2015) G. Bartoli et al.   ANNALS OF BOTANY

Transcript profiles in cortical cells of maize primary root during ethylene-induced lysigenous aerenchyma formation under aerobic conditions

(2015) Hirokazu Takahashi et al.   ANNALS OF BOTANY

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Establishment of an efficient micropropagation and callus regeneration system from the axillary buds of Bambusa ventricosa

(2015) Qiang Wei et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Capturing spiral radial growth of conifers using the superellipse to model tree-ring geometric shape

(2015) Pei-Jian Shi et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

BeMADS1 is a key to delivery MADSs into nucleus in reproductive tissues-De novo characterization of Bambusa edulis transcriptome and study of MADS genes in bamboo floral development

(2014) Ming-Che Shih et al.   BMC PLANT BIOLOGY

Enhanced cold stress tolerance of transgenic Dendrocalamus latiflorus Munro (Ma bamboo) plants expressing a bacterial CodA gene

(2014) Guirong Qiao et al.   IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY-PLANT

Leaf-shape remodeling: programmed cell death in fistular leaves ofAllium fistulosum

(2014) Xi-Lu Ni et al.   PHYSIOLOGIA PLANTARUM

Characterization of the Floral Transcriptome of Moso Bamboo (Phyllostachys edulis) at Different Flowering Developmental Stages by Transcriptome Sequencing and RNA-Seq Analysis

(2014) Jian Gao et al.   PLoS One

Programmed cell death during aerenchyma formation in Typha angustifolia leaves

(2013) Xi-Lu Ni et al.   AQUATIC BOTANY

Next-generation sequencing-based mRNA and microRNA expression profiling analysis revealed pathways involved in the rapid growth of developing culms in Moso bamboo

(2013) Cai-yun He et al.   BMC PLANT BIOLOGY

Ethylene and reactive oxygen species are involved in root aerenchyma formation and adaptation of wheat seedlings to oxygen-deficient conditions

(2013) Takaki Yamauchi et al.   JOURNAL OF EXPERIMENTAL BOTANY

Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data

(2013) MARC LOHSE et al.   PLANT CELL AND ENVIRONMENT

Identification of an AtCRN1-like chloroplast protein BeCRN1 and its distinctive role in chlorophyll breakdown during leaf senescence in bamboo (Bambusa emeiensis ‘Viridiflavus’)

(2013) Qiang Wei et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Transcriptome Sequencing and Analysis of the Fast Growing Shoots of Moso Bamboo (Phyllostachys edulis)

(2013) Zhenhua Peng et al.   PLoS One

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

De Novo Sequencing and Characterization of the Floral Transcriptome of Dendrocalamus latiflorus (Poaceae: Bambusoideae)

(2012) Xue-Mei Zhang et al.   PLoS One

Transcriptome Sequencing and De Novo Analysis for Ma Bamboo (Dendrocalamus latiflorus Munro) Using the Illumina Platform

(2012) Mingying Liu et al.   PLoS One

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

Morphological classification of plant cell deaths

(2011) W G van Doorn et al.   CELL DEATH AND DIFFERENTIATION

Identification of genes expressed in maize root cortical cells during lysigenous aerenchyma formation using laser microdissection and microarray analyses

(2010) Imene Rajhi et al.   NEW PHYTOLOGIST

Aerenchyma formation in the rice stem and its promotion by H2O2

(2010) Bianka Steffens et al.   NEW PHYTOLOGIST

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Formation of intercellular gas space in the diaphragm during the development of aerenchyma in the leaf petiole of Sagittaria trifolia

(2007) Feng Liang et al.   AQUATIC BOTANY