“If the gene is broadly expressed in many cell types across the organism, it may be difficult to change expression,” he said. “But if the gene expression is limited to a single cell type or a few cell types, maybe it can succeed.”

When gene expression did diverge between the two worms, the changes were more likely to occur in specialized cell types. For example, expression patterns in cells involved in basic functions like muscle or gut tended to be conserved, while expression patterns in more specialized cells involved in sensing and responding to the worm’s environment were more likely to diverge.

“Genes related to neuronal function, for example, seem to diverge more rapidly—perhaps because changes were needed to adapt to new environments—but for now, that’s speculation,” said Christopher R. L. Large, a postdoctoral fellow in the Department of Genetics at the Perelman School of Medicine at the University of Pennsylvania and the paper’s lead author.

Large earned his Ph.D. in genome sciences from the UW School of Medicine.

In the study, researchers compared gene expression patterns in two soil-dwelling roundworms, Caenorhabditis elegans and Caenorhabditis briggsae. Both species are ideal for studying development: They are small, about a millimeter long; simple, made up of about 550 cells when fully developed; and transparent. These characteristics allow scientists to observe their cells divide and develop in real time. Importantly, these worms share many of their roughly 20,000 genes with more complex organisms, including humans.

All the cells in both worms have been identified and mapped. Despite 20 million years of evolution, the two worms retain nearly identical body plans and cell types, with an almost one-to-one correspondence that makes them ideal subjects for comparison.

The goal of the study was to compare gene expression in every cell type of the two worms to determine what changes had occurred since they split from their common ancestor.

To do this, the researchers measured levels of messenger RNA in every cell at various stages of embryonic development by using a technique called single-cell RNA sequencing.

Messenger RNA, or mRNA, carries the instructions for making proteins from active genes to the cell’s protein-making machinery. High levels of mRNA from a gene indicate it is active. Low levels mean it is inactive.

With the single-cell RNA sequencing technique, the researchers tracked the changes in the individual cells through the worms’ embryonic development from when the embryo was a ball of 28 mostly undifferentiated cells to when most cell types had developed into their near final form, a process that takes about 12 hours.

A developmental cell atlas for two nematode species

The transcriptomes of single cells from C. elegans and C. briggsae were collected, annotated, and compared to identify differences in expression conservation for cell types and genes. The lineage-resolved transcriptomic atlases were used to measure the conservation of gene regulatory networks, contrast the timing of gene expression between species, and classify gene duplications based on expression and protein conservation.

“We’ve been studying the evolution of development since the 1970s,” said Dr. Junhyong Kim, professor of biology and director of the Penn Genome Frontiers Institute, who is a co-senior author of the study. “But this is the first time that we’ve been able to compare development in every single cell of two different organisms.”

Kim said the finding that some gene expression was conserved wasn’t surprising, because of how similar the worms’ bodies are. But it was surprising that when there were changes, those changes appeared to have no effect on the body plan.

The study describes where and when gene expression patterns differ between the species but doesn’t yet explain why, said Dr. John Isaac Murray, associate professor of genetics at the Perelman School of Medicine and the study’s third senior author.

“It’s hard to say whether any of the differences we observed were due to evolutionary adaptation or simply the result of genetic drift, where changes happen randomly,” Murray said. “But this approach will allow us to explore many unanswered questions about evolution.”

Source – UW School of Medicine