Étienne Danchin

This study identifies parallel large deletions in virulent M. incognita isolates that correlate with gene loss and virulence against Mi-1.2 resistance in tomato.

This study combines HiFi long-read and short-read sequencing to improve MAG recovery and binning accuracy in soil microbiomes.

This paper investigates how Meloidogyne incognita infects diverse plant species by analyzing transcriptomic responses across nine plant interactions, finding distinct transcriptional programs and effector deployment patterns that influence host specificity.

The paper identifies and characterizes orphan genes in eight root-knot nematode species, finding they contribute to parasitism and are expressed during the infective juvenile stage.

The paper presents the telomere-to-telomere genome of Xiphinema index, revealing HGTs related to plant parasitism and an unprecedented epigenetic toolkit in nematodes.

The paper evaluates transformer-based models' ability to predict structural features of orphan proteins and finds they perform poorly on these sequences compared to homologous proteins.

This paper develops an optimized dCas9-based CAPTURE method for studying DNA-protein interactions in the nematode Meloidogyne incognita, identifying chromatin-associated proteins involved in effector gene regulation.

This study presents a chromosome-scale genome assembly of Meloidogyne hapla, revealing recombination hotspots enriched with effector proteins involved in parasitism.

This study identifies genomic rearrangements in Meloidogyne graminicola, revealing evidence of meiotic recombination and a dual reproductive mode contributing to its adaptability.

The paper presents a high-quality genome assembly of Meloidogyne enterolobii using long-read sequencing and a gap-aware transformer model.

The paper identifies plant-derived horizontal gene transfer (HGT) events in Bemisia tabaci, revealing functional CAZymes with distinct glucanase activities.

The paper introduces MOnSTER, a tool for clustering and scoring protein sequence motifs, and applies it to identify specific motifs in plant-parasitic nematode effectors.

The paper assembles polyploid nematode genomes using long-read sequencing and identifies novel telomeric repeats that replace the conserved (TTAGGC)n sequence.

This study compares the transcriptomic responses of bdelloid rotifers to desiccation and ionizing radiation, finding shared and distinct molecular mechanisms.

AvP automatically detects candidate horizontal gene transfers using a phylogenetic framework, streamlining the process of identifying and analyzing HGTs.

The paper identifies susceptibility genes involved in trans-kingdom vitamin B synthesis between a plant-parasitic nematode and its host, revealing a horizontal gene transfer critical for parasitism.

The paper improves eukaryotic protein prediction and taxonomic annotation from soil metagenomes by using eukaryote-tailored methods, resulting in a more accurate representation of eukaryotic biodiversity.

This study investigates histone modifications in the plant-parasitic nematode Meloidogyne incognita to understand their role in development and parasitism, revealing their impact on gene expression and chromatin structure.

The paper analyzes the spatio-temporal gene expression of Meloidogyne incognita across its life stages and identifies a conserved promoter motif associated with effector genes.

The paper sequences and analyzes the genome of M. enterolobii, revealing a polyploid structure and transposable element abundance similar to other mitotic parthenogenetic Meloidogyne species.

The paper analyzes GH45 proteins from Phytophaga beetles to determine their enzymatic functions and evolutionary origins, finding they degrade multiple substrates and were horizontally transferred from fungi.