Rory J. Craig

This study analyzes over 300 plant mitochondrial genomes to show that gene content is conserved but structural complexity varies, driven by repeat proliferation and recombination rather than intergenomic DNA transfer.

The paper investigates how a giant virus maintains latency in a green alga by analyzing its genomic architecture and epigenetic regulation.

The paper identifies population-specific selective sweeps in Chlamydomonas reinhardtii, showing that positive selection maintains genetic structure despite gene flow.

The paper presents a lineage-wide evolutionary analysis of 3D genome architecture and organization across brown algae, revealing conserved chromosomal features, lineage-specific rearrangements, and long-term co-evolution of centromeres and retrotransposons.

This study presents a diploid genome assembly and genetic toolkit for Auxenochlorella, revealing evolutionary forces like mitotic recombination and loss-of-heterozygosity, and demonstrating its utility for research and bioengineering.

The paper shows that endogenous viral elements in brown algae can reactivate, replicate, and transmit viruses, challenging the view of EVEs as inert.

The paper introduces ERGO, a method for random gene overexpression in Chlamydomonas to study gene function, identifying CMRP1 as a regulator of carotenoid metabolism.

The paper analyzes brown algal genomes to trace the origin and evolution of U/V sex chromosomes, revealing gene gain-driven evolution and the demise of these systems through hermaphroditism and gene hierarchy shifts.

The paper presents a chromosome-level genome assembly of Bostrychia moritziana, revealing genome size expansion and genetic adaptations in red algae.

The paper identifies an active giant endogenous virus in Chlamydomonas reinhardtii, showing viral production and latent infection dynamics in natural isolates.

The paper identifies leaky ribosomal scanning as the mechanism enabling tunable translation of bicistronic ORFs in green algae through bioinformatic and in vivo analyses.

The paper maps the 3D chromatin structure of sex chromosomes in the brown alga Ectocarpus, revealing their spatial organization and links to gene expression and sex determination.

The paper traces the evolutionary origin of eukaryotic RNA-guided endonucleases, showing they evolved from a specific clade of bacterial IS607 TnpB enzymes.

The paper analyzes two extremophilic algae to understand their iron management strategies, identifying novel iron-uptake proteins and adaptive mechanisms that enable survival in low-iron environments.

The paper presents version 6 of the Chlamydomonas reinhardtii reference genome, improving assembly quality and revealing structural mutations in laboratory strains.

The paper identifies a new clade of Penelope-like retroelements with permuted domains, showing broad distribution across invertebrates and green lineage organisms.

The paper describes the subtelomere architecture in Chlamydomonas reinhardtii using long-read sequencing and identifies repeated elements and their evolutionary dynamics.

The paper presents genome assemblies for three Chlamydomonas species and identifies conserved elements and centromeric repeats, enhancing comparative genomics resources for this model organism.