Papain-like cysteine proteases in Carica papaya: lineage-specific gene duplication and expansion

Papain-like cysteine proteases as hubs in plant immunity

(2016) Johana C. Misas-Villamil et al.   NEW PHYTOLOGIST

Transcriptome analysis of the male-to-hermaphrodite sex reversal induced by low temperature in papaya

(2016) Hai Lin et al.   Tree Genetics & Genomes

The Tomato yellow leaf curl virus (TYLCV) V2 protein inhibits enzymatic activity of the host papain-like cysteine protease CYP1

(2015) Amalia Bar-Ziv et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Coevolution can explain defensive secondary metabolite diversity in plants

(2015) Michael P. Speed et al.   NEW PHYTOLOGIST

The battle in the apoplast: further insights into the roles of proteases and their inhibitors in plant–pathogen interactions

(2015) Mansoor Karimi Jashni et al.   Frontiers in Plant Science

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Cysteine protease and cystatin expression and activity during soybean nodule development and senescence

(2014) Stefan George van Wyk et al.   BMC PLANT BIOLOGY

Compatibility in the Ustilago maydis–Maize Interaction Requires Inhibition of Host Cysteine Proteases by the Fungal Effector Pit2

(2013) André N. Mueller et al.   PLoS Pathogens

A dated phylogeny of the papaya family (Caricaceae) reveals the crop’s closest relatives and the family’s biogeographic history

(2012) Fernanda Antunes Carvalho et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

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

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

Subclassification and Biochemical Analysis of Plant Papain-Like Cysteine Proteases Displays Subfamily-Specific Characteristics

(2012) K. H. Richau et al.   PLANT PHYSIOLOGY

Evaluation of New Reference Genes in Papaya for Accurate Transcript Normalization under Different Experimental Conditions

(2012) Xiaoyang Zhu et al.   PLoS One

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

Phytophthora infestans effector AVRblb2 prevents secretion of a plant immune protease at the haustorial interface

(2011) T. O. Bozkurt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Biochemical and molecular characterization of senescence-related cysteine protease-cystatin complex from spinach leaf

(2010) Takayuki Tajima et al.   PHYSIOLOGIA PLANTARUM

An Effector-Targeted Protease Contributes to Defense against Phytophthora infestans and Is under Diversifying Selection in Natural Hosts

(2010) F. Kaschani et al.   PLANT PHYSIOLOGY

Dosage Sensitivity Shapes the Evolution of Copy-Number Varied Regions

(2010) Benjamin Schuster-Böckler et al.   PLoS One

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Latex: A Model for Understanding Mechanisms, Ecology, and Evolution of Plant Defense Against Herbivory

(2009) Anurag A. Agrawal et al.   Annual Review of Ecology Evolution and Systematics

DnaSP v5: a software for comprehensive analysis of DNA polymorphism data

(2009) P. Librado et al.   BIOINFORMATICS

Phylogenomic analysis of the cystatin superfamily in eukaryotes and prokaryotes

(2009) Dušan Kordiš et al.   BMC EVOLUTIONARY BIOLOGY

Gene duplication and evolutionary novelty in plants

(2009) Lex E. Flagel et al.   NEW PHYTOLOGIST

MEROPS: the peptidase database

(2009) Neil D. Rawlings et al.   NUCLEIC ACIDS RESEARCH

Characterization of the Entire Cystatin Gene Family in Barley and Their Target Cathepsin L-Like Cysteine-Proteases, Partners in the Hordein Mobilization during Seed Germination

(2009) M. Martinez et al.   PLANT PHYSIOLOGY

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus)

(2008) Ray Ming et al.   NATURE

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY