In a new study, researchers at The University of Tokyo have discovered surprising variations in genome size within the Closterium peracerosum-strigosum-littorale (C. psl.) complex, a group of unicellular algae closely related to land plants. The findings, published in Genome Biology and Evolution, have opened new avenues for exploration in genome dynamics among microeukaryotes.
The typical notion of genomic stability and variability is based on observations in a handful of model organisms. For instance, genome size, although varying greatly across the tree of life, has generally been considered stable within species or closely related organisms. But Takashi Tsuchimatsu and Yawako Kawaguchi's research on C. psl. complex has shown a more complex picture.
While conducting standard population and comparative genomic analyses of 22 natural strains of C. psl., the team found that the genomes were far more intricate than initially thought. "Our most exciting finding was that there is extensive genome size variation between closely related algal strains that are morphologically indistinguishable," says Tsuchimatsu.
The studied strains displayed a more than twofold variation in genome size, ranging from 450 to over 1,100 megabases. This unexpected discovery caused the researchers to pivot their investigation toward understanding the reasons behind such an extensive variation in genome size.
Through further analysis, Tsuchimatsu and his team found that genome-wide copy number variation (CNV) plays a vital role in driving this extensive genome size dynamics. CNVs result from the duplication or deletion of genes or large DNA segments. Around 30% of the genes were found to vary in copy number, even among closely related strains of C. psl., signifying that swift changes in genome size were influenced by frequent duplications and deletions across the genome.
Interestingly, the researchers found that gene expression levels did not always correspond with gene copy numbers for about 30% of the genes exhibiting CNV. This discovery points to an epigenetic process like dosage compensation that maintains balanced gene expression despite changes in gene dosage. By allowing for greater variation in genome size, dosage compensation may preserve extensive CNV within the C. psl. complex.
However, the exact mapping of duplicate sequences across chromosomes remains a challenge. Tsuchimatsu acknowledges, "Observing chromosomes at high resolution is still tricky in Closterium," but recent observations have hinted at mechanisms tolerating chromosomal rearrangements during meiosis.
Additional research into genome dynamics, both in C. psl. complex and other non-model species might explain the conventional rules of genomic stability, revealing eukaryotic genomes to be more dynamic than previously believed. This study also aligns with recent findings in other algae research, together presenting compelling evidence that eukaryotic genomes may house untold complexities waiting to be uncovered. The work done by Tsuchimatsu, Kawaguchi, and their colleagues brings us closer to understanding the nuanced interactions within genomes that enrich our grasp of biology's fundamental processes.