Comparison of first complete non-human chromosome show that the human Y chromosome is shrinking

X and Y chromosomes in green with yellow tips by Nathan Devery from-Shutterstock via The Conversation.png
X and Y chromosomes in green by Nathan Devery from Shutterstock via The Conversation.png
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Scientists generate the first complete chromosome sequences from six non-human primates, including both X and Y chromosomes. The sequence has revealed new insights into evolution and has indicated that the human Y chromosome is shrinking. The team fro the National Insitutes of Health published their findings in Nature.

These newly sequenced chromosomes reveal striking diversity among Y chromosomes across species, highlighting their rapid evolutionary changes. Additionally, they shed light on previously unexplored regions of great ape genomes. Given that these primate species are our closest living relatives, these novel sequences offer valuable insights into human evolution.The scientific team concentrated their efforts on the X and Y chromosomes, which are crucial for sexual development, fertility, and numerous other biological processes. Their study encompassed the sequencing of chromosomes from six primate species:

  1. Chimpanzee
  2. Bonobo
  3. Gorilla
  4. Bornean orangutan
  5. Sumatran orangutan
  6. Siamang gibbon (a more distantly related primate species)

This comprehensive approach allows for a broader understanding of primate genomics and its implications for human evolutionary history.

“These chromosome sequences add a significant amount of new information,” said Brandon Pickett, Ph.D., a postdoctoral fellow at the National Human Genome Research Institute (NHGRI), part of NIH, and an author of the study. “Only the chimpanzee genome sequence was fairly complete before this, but even that still had large gaps, especially in regions of repetitive DNA.”

The analysis of the new sequences revealed that 62 to 66 percent of the X chromosomes and 75 to 82 percent of the Y chromosomes are composed of repetitive DNA sequences. Because repetitive sequences are much more challenging to characterise, this has only been possible in recent years due to new DNA sequencing technologies and analysis methods.

The investigation revealed fascinating insights into the conservation and divergence of genetic material over millions of years.

Key Findings

  1. Gene Disparity: Similar to humans, the Y chromosomes in great apes contain significantly fewer genes compared to their X chromosome counterparts.
  2. X Chromosome Conservation: Over 90% of the ape X chromosome sequences aligned with the human X chromosome. This high degree of similarity indicates that X chromosomes have remained remarkably stable throughout the course of evolution.
  3. Y Chromosome Divergence: In stark contrast, only 14% to 27% of the ape Y chromosome sequences aligned with the human Y chromosome, suggesting substantial evolutionary changes in this chromosome.

Methodology

The researchers employed a computational technique called alignment to identify regions of chromosomes that have remained consistent over evolutionary time. This method allows scientists to:

  • Pinpoint areas of genetic stability
  • Detect regions that have undergone significant changes
  • Infer the effects of various evolutionary pressures on different parts of the genome

This comparative genomic approach has provided valuable insights into the evolutionary trajectories of sex chromosomes in great apes and humans, highlighting both conserved features and areas of divergence.

“The extent of the differences between the Y chromosomes of these species was very surprising,” said Kateryna Makova, Ph.D., a professor at Pennsylvania State University and leader of the study. “Some of these species diverged from the human lineage only seven million years ago, which is not a lot of time in terms of evolution. This shows that the Y chromosomes are evolving very fast.”

According to the statement:

“A notable difference among the primate Y chromosomes is their length. For example, the Y chromosome from the Sumatran orangutan is twice as long as the gibbon’s Y chromosome. Variation in the number and types of DNA repeats accounts for some of the differences in chromosome lengths.

One type of repeat is called a palindrome, a DNA sequence which contains inverted DNA repeats. DNA palindromes are similar to language palindromes such as “racecar” or “kayak,” in which the letters in the first half of the word repeat in reverse in the second half of the word, so the sequence of the letters is the same forwards and backwards. However, the DNA palindromes can be over one hundred thousand letters long.

The researchers found that the DNA palindromes on the primate X and Y chromosomes almost always contain genes, which repeat in many copies along the length of the chromosome. Most genes in primate genomes have only two copies, one on each chromosome in a pair. Researchers suspect that having many copies in these palindromes helps to protect genes, especially on the Y chromosome. Since there is typically only one Y chromosome per cell, if a gene on the Y chromosome is damaged, there is not another chromosome with a copy of the gene that can be used as a template to repair the damage.”

“Having these genes in palindromes is like keeping a backup copy,” said Adam Phillippy, Ph.D., a senior investigator at NHGRI and senior author of the study. “We know that many of these genes are performing important functions, and so we expected to see the same genes in palindromes across different species, but this doesn’t seem to be the case.”

The researchers investigated various groups of genes located within palindromic sequences, many of which are involved in sperm production and are crucial for fertility. Although palindromic sequences were present on the Y chromosomes of all primates examined, the exact sequences and the genes they contained were often unique to each species.

“There may be even more variation we’re not yet seeing,” said Dr. Phillippy. “On the human Y chromosome, some genes can vary in number between individuals. For each of these other primate species, we’re only looking at a single individual. We don’t know what the rest of the population looks like yet and what other variations we might find.”

“However, we have some insights from prior work by our group that suggests extensive variation in the number of copies of Y chromosome genes in humans and other apes,” Dr. Makova added.

The statement also highlighted: “These great ape chromosome sequences also resolve the sequences of another type of repeat called a DNA satellite, which is a large stretch of repeating sequence. Among the great ape chromosomes, the researchers identified several previously unknown, species-specific satellite sequences.

These sequences provide important insights into great ape genomes, as DNA satellites are present across the genome. Specifically, they are concentrated near the ends of chromosomes, called telomeres, and in another region called a centromere, which helps the chromosomes organize during cell division. The centromere sequences of these species were completely unknown before this study and another recent research effort conducted by many of the same researchers.”

“Having these satellite sequences from great apes open up new territory to explore,” said Dr. Makova, “and similar to our other findings about the Y chromosome, we can see that the centromere of the Y chromosome is highly dynamic.”

These chromosome sequences are crucial for researchers studying the evolution of great apes, including humans. While researchers aim to describe the entire genomes of these species, the X and Y chromosome sequences alone provide significant insights. Notably, they reveal evolutionary forces acting on the Y chromosome that drive its rapid evolution.

One factor is that typically, there is only one Y chromosome per cell, leading to the accumulation of changes in its DNA sequence. Another factor, according to Dr. Makova, is male mutation bias. Unlike egg production, sperm production involves more frequent DNA replication, increasing the chances of DNA sequence changes with each replication. This phenomenon impacts all chromosomes but has a pronounced effect on the Y chromosome.

Additionally, the small population sizes of great ape species influence their evolutionary rates. In the wild, these species have limited populations, and since Y chromosomes are present only in males, this further reduces the effective population size of this part of the genome.

“It’s important to remember that these great ape species are all endangered,” said Dr. Makova. “Not only can we learn about human evolution from these sequences, but we can apply what we know about their genomes and human genomes to better understand the biology and reproduction of these endangered species.”

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I am a Chartered Environmentalist from the Royal Society for the Environment, UK and co-owner of DoLocal Digital Marketing Agency Ltd, with a Master of Environmental Management from Yale University, an MBA in Finance, and a Bachelor of Science in Physics and Mathematics. I am passionate about science, history and environment and love to create content on these topics.