André Marques

Ayahuasca plant genomes reveal retrotransposon-derived centromeres and contrasting routes to DMT and β-carbolines

The paper presents the genomes of Ayahuasca source plants, revealing retrotransposon-derived centromeres and distinct biosynthetic pathways for DMT and beta-carbolines.

An atlas of eukaryotic centromere architecture reveals recurrent evolutionary dynamics

Across 325 Darwin Tree of Life genomes, satellite-array and transposon-cluster centromeres are phylogenetically scattered, fitting a model of repeated interconversion; satellites share higher-order repeat structure but not sequence.

The Nature of Centromeric Repeat Turnovers in the genus Arabidopsis

This study identifies centromeric repeat turnovers in Arabidopsis species, revealing evolutionary mechanisms and the role of genetic drift and centromere drive in repeat replacement.

The Spirogyra genome: signatures of shared and divergent division and differentiation

This study sequenced the Spirogyra pratensis genome and analyzed its transcriptional responses to light and temperature, revealing unique cytokinetic processes and plastid division mechanisms.

Dynamic holocentric genomes facilitate divergent evolutionary paths through chromosomal rearrangements, hybrid dysfunction, and recombination suppression

This study investigates chromosomal rearrangements in Carex laevigata, showing they arise in structurally fragile regions and contribute to genomic divergence through hybrid dysfunction and recombination suppression.

Nowhere to Hide: The Effect of Centromere Architecture on LTR Retrotransposon Dynamics

This study tests a 'nowhere-to-hide' model linking centromere architecture to LTR retrotransposon dynamics, finding that holocentric chromosomes show different patterns of element persistence and removal compared to monocentric ones.

Genomic insights into the karyotypic radiation of a narrow endemic holocentric plant Carex helodes

The paper examines chromosomal rearrangements in Carex helodes, identifying genomic features associated with karyotypic evolution and environmental adaptation.

Haplotype-specific chromosome painting unveils recombination patterns in the holocentric species Rhynchospora breviuscula H.Pfeiff.

This study uses haplotype-specific chromosome painting to map meiotic recombination patterns in holocentric plants, revealing that recombination events are predominantly located in terminal chromosomal regions.

Stepwise emergence of recombination suppression precedes fissiparous asexuality in the planarian Schmidtea mediterranea

This study shows that recombination suppression through chromosomal rearrangements preceded fissiparous asexuality in planarians, reducing the costs of asexuality.

Holocentromere diversity in Cyperaceae: contrasting repeat organisation in Mapanioideae and Cyperoideae

This study compares holocentromere organization in two Cyperaceae subfamilies, revealing differences in repeat structure and protein distribution associated with centromere function.

How much can reticulate evolution entangle plant systematics? Revisiting subfamilial classification of the Malvatheca clade (Malvaceae) on the basis of phylogenomics

The paper uses phylogenomic analysis to study reticulate evolution in the Malvatheca clade, finding evidence of ancient hybridization and polyploidy affecting subfamilial classification.

Sex without crossovers mimics clonal reproduction in the holocentric plant Rhynchospora tenuis

This study shows that Rhynchospora tenuis undergoes obligate achiasmy in both sexes, leading to clonal-like inheritance through post-meiotic selection and TE-driven segregation distortion.

A holocentric pangenome links karyotype evolution to meiotic recombination

The paper links karyotype evolution to meiotic recombination by analyzing holocentric genomes and crossover patterns in Rhynchospora species.

Pangenome analysis reveals the evolutionary dynamics of repeat-based holocentromeres

The paper analyzes Tyba satellite DNA repeats and transposable elements in holocentric species to reveal evolutionary dynamics of repeat-based holocentromeres across a pangenome.

Chromosome Size as a Robust Predictor of Recombination Rate: Insights from Holocentric and Monocentric Systems

The paper identifies chromosome number and mean chromosome size as proxies for recombination rate using genetic map data from 73 insect species and 157 monocentric plants, showing mean size is a better predictor, especially in holocentric species.

Centromere divergence and allopolyploidy reshape carnivorous sundew genomes

The paper investigates how centromere divergence and allopolyploidy influence genome evolution in carnivorous sundews, revealing structural differences between species with distinct chromosomal architectures.

Impaired trap closure in the counting-deficient Venus flytrap mutant DYSCALCULIA is caused by cell wall biomechanics

This study identifies impaired cell wall biomechanics as the cause of delayed trap closure in the Venus flytrap mutant DYSCALCULIA, linking mechanosensing and Ca2+ signaling to trap kinetics.

A comparative analysis of planarian genomes reveals regulatory conservation in the face of rapid structural divergence

This paper presents chromosome-scale genome assemblies and regulatory element annotations for planarians, revealing conservation of regulatory regions despite rapid structural divergence.

Repeat-based holocentromeres of the woodrush Luzula sylvatica reveal new insights into the evolutionary transition from mono- to holocentricity

The paper identifies repeat-based holocentromeres in Luzula sylvatica and proposes mechanisms for the evolutionary transition from monocentric to holocentric chromosomes.

KNL1 and NDC80 represent new universal markers for the detection of functional centromeres in plants

The paper introduces antibodies against KNL1 and NDC80 as more versatile markers for detecting functional centromeres in plants compared to CENH3 antibodies.

Meiotic recombination dynamics in plants with repeat-based holocentromeres shed light on the primary drivers of crossover patterning

The paper investigates meiotic recombination dynamics in a holocentric plant, finding that telomere-led pairing drives a U-shaped crossover distribution, independent of centromere organisation.

Oligo-barcodes illuminate holocentric karyotype evolution in Rhynchospora (Cyperaceae)

The paper develops oligo-based barcode probes for holocentric chromosomes in Rhynchospora and uses them to analyze karyotype evolution across species.

Aiming off the target: studying repetitive DNA using target capture sequencing reads

This study evaluates the effectiveness of target capture sequencing (TCS) for characterizing repetitive DNA in Rhynchospora species, showing reliable results comparable to genome skims.

Genome sequence of the cluster root forming white lupin

The paper provides a high-quality genome sequence of white lupin and identifies a transcription factor regulating cluster root formation.