Jir̆ı́ Macas

TideCluster is a pipeline for clustering and classifying tandem repeats across genomes, demonstrated on Arabidopsis and Solanum species.

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 paper presents an improved pea genome assembly using long-read sequencing and other techniques, resulting in a highly contiguous and complete genome resource.

The paper compares centromere organization and (epi)genome features between two species with different centromere types, finding distinct histone phosphorylation patterns and kinetochore gene mutations.

The paper introduces DANTE and DANTE_LTR pipelines for annotating LTR retrotransposons in plant genomes, showing improved accuracy in identifying intact elements compared to existing methods.

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

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

The paper assembles and analyzes the 81.6 Mb centromere of pea chromosome 6, revealing its structure and evolutionary mechanisms in metapolycentric chromosomes.

This study shows that holocentric Cuscuta species have lost the standard kinetochore and SAC, with gene loss and protein mislocalization observed.

The paper examines genome size variation and centromere organization in Cuscuta species, finding that holocentric chromosomes are associated with reduced genome size and changes in repetitive DNA and epigenetic marks.

The paper uses a multi-omics approach to analyze the structure, expression, and methylation of rRNA loci in wheat, revealing tissue-specific expression patterns and silencing mechanisms.

The paper develops an assembly-free method using nanopore reads to characterize satellite DNA arrays in Lathyrus sativus, revealing differences in their organization and association with LTR-retrotransposons.

The paper investigates the mechanism of B chromosome drive in Aegilops speltoides, identifying nondisjunction and asymmetric spindles as key factors in their accumulation.