The Transcriptomes of Xiphinema index and Longidorus elongatus Suggest Independent Acquisition of Some Plant Parasitism Genes by Horizontal Gene Transfer in Early-Branching Nematodes

Disparate gain and loss of parasitic abilities among nematode lineages

(2017) Martijn Holterman et al.   PLoS One

Hybridization and polyploidy enable genomic plasticity without sex in the most devastating plant-parasitic nematodes

(2017) Romain Blanc-Mathieu et al.   PLoS Genetics

Alienness: Rapid Detection of Candidate Horizontal Gene Transfers across the Tree of Life

(2017) Corinne Rancurel et al.   Genes

TransRate: reference-free quality assessment of de novo transcriptome assemblies

(2016) Richard Smith-Unna et al.   GENOME RESEARCH

Horizontal Gene Transfer from Bacteria Has Enabled the Plant-Parasitic NematodeGlobodera pallidato Feed on Host-Derived Sucrose

(2016) Etienne G.J. Danchin et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome Skimming: A Rapid Approach to Gaining Diverse Biological Insights into Multicellular Pathogens

(2016) Dee R. Denver et al.   PLoS Pathogens

Evolution of Plant Parasitism in the Phylum Nematoda

(2015) Casper W. Quist et al.   Annual Review of Phytopathology

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

(2015) Felipe A. Simão et al.   BIOINFORMATICS

The Pfam protein families database: towards a more sustainable future

(2015) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Distribution and evolution of glycoside hydrolase family 45 cellulases in nematodes and fungi

(2014) Juan E Palomares-Rius et al.   BMC EVOLUTIONARY BIOLOGY

The Transcriptome of Nacobbus aberrans Reveals Insights into the Evolution of Sedentary Endoparasitism in Plant-Parasitic Nematodes

(2014) Sebastian Eves-van den Akker et al.   Genome Biology and Evolution

Characterisation of the transcriptome of Aphelenchoides besseyi and identification of a GHF 45 cellulase

(2014) Tiasei Kikuchi et al.   NEMATOLOGY

Signatures of adaptation to plant parasitism in nematode genomes

(2014) DAVID McK. BIRD et al.   PARASITOLOGY

The genome and life-stage specific transcriptomes of Globodera pallida elucidate key aspects of plant parasitism by a cyst nematode

(2014) James A Cotton et al.   GENOME BIOLOGY

The complex hybrid origins of the root knot nematodes revealed through comparative genomics

(2014) David H. Lunt et al.   PeerJ

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

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

Top 10 plant-parasitic nematodes in molecular plant pathology

(2013) John T. Jones et al.   MOLECULAR PLANT PATHOLOGY

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

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space

(2012) Fredrik Ronquist et al.   SYSTEMATIC BIOLOGY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Horizontal Gene Transfer in Nematodes: A Catalyst for Plant Parasitism?

(2011) Annelies Haegeman et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

The draft genome of the parasitic nematode Trichinella spiralis

(2011) Makedonka Mitreva et al.   NATURE GENETICS

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

Genomic Insights into the Origin of Parasitism in the Emerging Plant Pathogen Bursaphelenchus xylophilus

(2011) Taisei Kikuchi et al.   PLoS Pathogens

Genetic signature of amphimixis allows for the detection and fine scale localization of sexual reproduction events in a mainly parthenogenetic nematode

(2010) LAURE VILLATE et al.   MOLECULAR ECOLOGY

Multiple lateral gene transfers and duplications have promoted plant parasitism ability in nematodes

(2010) Etienne G. J. Danchin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

A phylogenetic tree of nematodes based on about 1200 full-length small subunit ribosomal DNA sequences

(2009) Hanny van Megen et al.   NEMATOLOGY

Identification and Characterization of the Most Abundant Cellulases in Stylet Secretions fromGlobodera rostochiensis

(2009) Sajid Rehman et al.   PHYTOPATHOLOGY

Analysis of a Horizontally Transferred Pathway Involved in Vitamin B6 Biosynthesis from the Soybean Cyst Nematode Heterodera glycines

(2008) J. P. Craig et al.   MOLECULAR BIOLOGY AND EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita

(2008) Pierre Abad et al.   NATURE BIOTECHNOLOGY

Sequence and genetic map of Meloidogyne hapla: A compact nematode genome for plant parasitism

(2008) C. H. Opperman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Massive Horizontal Gene Transfer in Bdelloid Rotifers

(2008) E. A. Gladyshev et al.   SCIENCE