According to the latest research published this week in the journal Science Advances, many modern marine invertebrates, such as sponges and jellyfish, contain chromosomes with the same old structure acquired from their primordial ancestors more than 600 million years ago.

The surprising discovery serves as a reminder that evolution is conservative, keeping things that operate well, such as gene arrangement on a chromosome, and provides a crucial connection between living organisms, including humans, and our distant ancestors.

“It emphasizes that even in something as fundamental as their chromosomes, diverse animals resemble each other,” says the paper’s senior author, Daniel Rokhsar. “That’s one of the reasons why we can learn so much about human biology from studying fruit flies, nematode worms, jellyfish and other ‘simple’ model systems — it’s because of the underlying unity of all animals. What we learn about animal diversity affects how we think about ourselves.”

The latest research predicts that the first multicellular creatures stored their genes in 29 pairs of ancient chromosomal units. Many of these chromosomes have survived intact for half a billion years. The first organisms originated in the waters and developed into varied invertebrates, from sponges to worms to humans.

On the other hand, humans have 46 chromosomes, the consequence of two duplications, many mergers, and chromosomal rearrangements dating back to the earliest mammals.

The research, led by Rokhsar and Oleg Simakov of the University of Vienna in Austria, is the first to compare the chromosomal positions of genes from a wide range of animals, including sponges, jellyfish, sea scallops, and other aquatic invertebrates, allowing for the inference of ancestral organisation and the study of rare changes in chromosome organisation. The chromosome-scale genomes of different invertebrates have recently been identified, although this type of research has been done for fruit flies and numerous vertebrates, including humans.

Conservative Evolution

The increasingly advanced techniques available these days help identify which genes are close to one another when the chromosome is curled up inside the nucleus. In recent years, scientists have begun assigning genes to chromosomes in several invertebrates: “the Florida lancelet, Branchiostoma floridae, a dainty, quill-like sea creature also known as amphioxus; a scallop, Patinopecten yessoensis; a freshwater sponge, Ephydatia muelleri; and the fire jellyfish, Rhopilema esculentum, a cnidarian. Rokhsar, Simakov and their team extended this set by determining the chromosomal sequences of a fifth animal, a hydra, Hydra vulgaris, another type of cnidarian.”

“What we find is remarkable: If you compare those five species with each other, you find that there’s extensive conservation; in many cases, whole chromosomes or big pieces of chromosomes have stayed together. A whole chromosome in a sponge might correspond to a chromosome in a jellyfish,” he expressed. “They’re not organized in exactly the same way — the genes are in a different order in the various species — but over these long-time scales, a chromosome behaves like a bag of genes that has maintained its integrity since the beginning of animal life; in the pre-Cambrian era.”

When they discovered that genes tended to stay together on the same chromosome in their sample of invertebrates — a phenomenon known as synteny, which comes from the Greek for “on the same thread” — they predicted that the same would be true of other invertebrates, such as sea urchins, worms, and mollusks. They discovered similar DNA conservation across chromosomes in these creatures when they looked at their chromosomes. All seemed to be descended from the same 29 chromosomal pairings seen in early animal relatives.

Implications for Humans and Other Vertebrates

“If you compare amphioxus to scallops and then representatives of a lot of different vertebrates — different kinds of fish, like lampreys, chickens, and so forth — you can see that there are 18 different groups of genes that seem to always stick together,” told Rokhsar. “They always travel together on the same piece of DNA, and so the simplest interpretation is that there were 18 ancestral chromosomes in the proto-vertebrate ancestor.”

Rokhsar and his colleagues have known for a long time that chromosomes were better conserved than previously supposed. He and his team have sequenced and examined the genomes of a sea squirt, a placozoan, a kind of lancelet, and different species of sponge, choanoflagellate, sea anemone, octopus, acorn worm, leech, limpet, and polychaete worm during the last 20 years. Despite the fact that the early “draft” genomes were typically fragmented, they exhibited hints of anciently preserved sets of genes connected across species. Newer technology that can determine whole chromosomes has verified those early assumptions.

The fact that genes from various invertebrates group together faithfully despite hundreds of millions of years of independent evolution could indicate that moving genes around among chromosomes is much more complex than scientists previously assumed based on their studies of vertebrates where genes rearranged more frequently, likely due to genetic drift.

“Animals like amphioxus live in huge populations where the rare mutants with rearranged chromosomes are at a disadvantage and typically die out, whereas, in small, subdivided populations, which is more typical of mammals, rearrangements are more likely to survive and spread. That’s one hypothesis,” said Rokhsar.

Alternatively, there might be an unexplained reason why some gene groups must stay together. The Hox genes, for example, govern which end of the animal embryo produces the head and which forms the tail, as well as all gradations in between. In most invertebrates, these genes are all grouped on one chromosome, critical for their deployment during development. The functional clustering of these genes, on the other hand, might be an outlier, and there’s no proof yet that the clusters discovered in the latest study are functionally connected, according to Rokhsar.

Image Description: The colored lines link similar genes across the chromosomes of five invertebrates — a scallop, a lancelet, a sponge, a jellyfish and a hydra. The amazing lack of crossover shows that genes have largely remained on the same chromosomes through over half a billion years of evolution. (Credit: Daniel Rokhsar, courtesy of Science)
Image Source: https://news.berkeley.edu/2022/02/04/reconstructing-the-chromosomes-of-the-earliest-animals-on-earth/

Because the complete genome was duplicated twice early in vertebrate evolution in the lineage leading to jawed vertebrates, including mammals, birds, reptiles, amphibians, and most fish, the simple conservation of chromosomes ends with invertebrates. A sequence of chromosomal reorganisations shaped the genomes of the first jawed vertebrates, which eventually gave rise to humans during these large-scale duplications. Rokhsar and collaborators bridge the vertebrate-invertebrate barrier and connect the first animal chromosomes with those of present vertebrates by following groups of genes as they transferred from one chromosome to another as the earliest vertebrates developed.

“One of the cool things is that once we infer these ancient proto-chromosomes and organize them on the tree of life, then we can make predictions. If you go and sequence some other genomes, we predict that you will inevitably find that these genes are mixed together on the same chromosome,” he said. “Unlike physics or chemistry, you don’t usually get to make such predictions in biology. But now we know something, in a sense, about almost all animal genomes from this comparison.”

Story Source: Oleg, S., Jessen, B., Kodiak, B., Ferdinand, M., Therese, M., T., S. D., … S., R. D. (2022). Deeply conserved synteny and the evolution of metazoan chromosomes. Science Advances, 8(5), eabi5884. https://doi.org/10.1126/sciadv.abi5884 https://news.berkeley.edu/2022/02/04/reconstructing-the-chromosomes-of-the-earliest-animals-on-earth/

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Dr. Tamanna Anwar is a Scientist and Co-founder of the Centre of Bioinformatics Research and Technology (CBIRT). She is a passionate bioinformatics scientist and a visionary entrepreneur. Dr. Tamanna has worked as a Young Scientist at Jawaharlal Nehru University, New Delhi. She has also worked as a Postdoctoral Fellow at the University of Saskatchewan, Canada. She has several scientific research publications in high-impact research journals. Her latest endeavor is the development of a platform that acts as a one-stop solution for all bioinformatics related information as well as developing a bioinformatics news portal to report cutting-edge bioinformatics breakthroughs.

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