Genomes of 51 animal species mapped in record time, creating ‘evolutionary time machine’
Researchers just mapped and published the genomes of 51 animal species, from fish-eating crocodiles known as gharials (Gavialis gangeticus) to fierce cloud leopards (Neofelis nebulosa). These genetic blueprints could have broad implications for humans, particularly for understanding our evolutionary history, according to a paper published Jan. 26 in the journal Nature Biotechnology.
“In some ways, we’re building an evolutionary time machine,” study co-author Michael Schatz, a Bloomberg distinguished professor of computer science and biology at Johns Hopkins University, said in a statement. “Having the genes of our evolutionary cousins mapped out will help us better understand ourselves.”
All mammals share a common ancestor, which many scientists believe to be Morganucodon, a tiny, shrew-like creature that lived more than 200 million years ago — though some say otherwise. In any case, this shared ancestor means that a large chunk of our genetic makeup resembles those of other mammals, particularly chimpanzees, which share up to 99% of our DNA. By comparing the DNA of humans and other animals, researchers can learn when and how humans diverged from other species.
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But a single vertebrate genome can be billions of characters long and researchers must use different tools to break this genetic material into chunks before piecing it into a full picture. As a result, mapping genomes has historically been a painstaking process: Beginning in 1990, it took researchers 13 years to create the first genetic blueprint for humans.
However, DNA mapping technology for different species has advanced rapidly in the past few decades, and this new project marks another step, cutting the sequencing time from years and months to just days.
To do this, the team used research from two projects: the Vertebrate Genomes Project and the European Reference Genome Atlas. From these they developed algorithms and computer software to assemble short genetic segments into a full genetic map, and eventually tested how well their workflow reproduced the complete genome of a zebra finch (Taeniopygia guttata), which had been previously published.
The team found that their new technology was more effective than existing approaches at reassembling segments of the genome and creating an accurate map. Their software is open-source and available online via Galaxy, a free, web-based platform based at Johns Hopkins and Pennsylvania State University.
“I think my first thought was, wow, they actually made this work,” Elinor Karlsson, director of the Vertebrate Genomics Group at the Broad Institute and a professor at the University of Massachusetts Medical School who was not involved in the study, told Live Science. “It’s really cool to actually see not only that they managed to come up with a system that seems to work well on pretty diverse species, but they’ve done it on a platform that is so committed to open science and sharing workflows.”
For this paper, the researchers focused only on vertebrates, and other animal, plant or fungal species might have “something distinctive or unique about their genome,” which means “some of the processes that are in this pipeline aren’t going to work as well in that species,” Karlsson said.
But this could be fixed “by modifying a few parameters” in their technique, according to the paper. The researchers’ goal is to sequence the genomes of at least one species across all 275 vertebrate orders.
