Estienne Carl Swart

Spliceosome loss in the red tide ciliate Mesodinium rubrum presents a symbiotic cul-de-sac

The paper analyzes the nuclear genomes of Mesodinium rubrum and finds it lacks spliceosomal introns and related machinery, suggesting introns hinder endosymbiotic genomic integration.

Emergent metabolic parasitism driven by organelle sequestration

The paper examines metabolic changes in Mesodinium species, finding that increased photosynthesis leads to reduced metabolic autonomy and loss of key biosynthetic capabilities.

ISWI1 complex proteins facilitate developmental genome editing in Paramecium

The paper identifies ICOP1 and ICOP2 as proteins interacting with ISWI1 that are essential for chromatin remodeling and DNA elimination during somatic genome development in Paramecium.

Nuclear dualism without extensive DNA elimination in the ciliate Loxodes magnus

This study investigates genome development in Loxodes magnus, finding no canonical IESs or editing hallmarks during MIC-to-MAC development, suggesting a loss or streamlining of genome editing processes.

Two paralogous PHD finger proteins participate inParamecium tetraurelia's natural genome editing

This study identifies two paralogous PHD finger proteins, DevPF1 and DevPF2, involved in DNA elimination during genome reorganization in Paramecium tetraurelia, with distinct roles in IES excision and small RNA regulation.

RNA-mediated nucleosome depletion is required for elimination of transposon-derived DNA.

The paper shows that ISWI-mediated nucleosome depletion and small RNAs are required for precise DNA elimination of transposon remnants in Paramecium.

Karyorelict ciliates use an ambiguous genetic code with context-dependent stop/sense codons

The paper identifies an ambiguous genetic code in karyorelict ciliates, where stop codons are reassigned to amino acids, and finds this code is used across multiple families.

MITE infestation of germline accommodated by genome editing in Blepharisma

The paper analyzes IESs in Blepharisma stoltei, revealing MITEs as a major source of IESs and challenging current models of transposon domestication in ciliates.

Genome editing excisase origins illuminated by somatic genome of Blepharisma

The paper reports the somatic genome of Blepharisma stoltei, identifying a PiggyBac transposase homolog as a potential IES excisase, suggesting an evolutionary origin for genome editing.

BleTIES: Annotation of natural genome editing in ciliates using long read sequencing

BleTIES annotates and analyzes internally eliminated sequences in ciliates using long-read sequencing data.