Complete X and Y chromosome sequences of living great ape species determined (2024)

Newly generated, complete "end-to-end" reference genomes for the sex chromosomes of five great ape species and one lesser ape species -- produced by an international collaborative team led by researchers at Penn State, the National Human Genome Research Institute and the University of Washington -- highlight extremely rapid changes on the male-specific Y chromosome among ape species. These findings shed light on the evolution of sex chromosomes and inform understanding of diseases related to genes on these chromosomes in both apes and humans.

"The Y chromosome is important for human fertility, and the X chromosome harbors genes critical for reproduction, cognition and immunity," said Kateryna Makova, Verne M. Willaman Chair of Life Sciences, professor of biology at Penn State and leader of the research team. "Our study opens doors for many future investigations of sex chromosomes, how they evolved, and diseases associated with them. The living non-human great ape species we studied are all endangered. The availability of their complete sex chromosome sequences will facilitate studies of their sex-specific dispersal in the wild and of their genes important for reproduction and fertility."

Such reference genomes act as a representative example that are useful for future studies of these species. The team found that, compared to the X chromosome, the Y chromosome varies greatly across ape species and harbors many species-specific sequences. However, it is still subject to purifying natural selection -- an evolutionary force that protects its genetic information by removing harmful mutations.

The new study appears May 29 in the journal Nature.

"Researchers sequenced the human genome in 2001, but it wasn't actually complete," Makova said. "The technology available at the time meant that certain gaps weren't filled in until a renewed effort led by the Telomere-to-Telomere, or T2T, Consortium in 2022-23. We leveraged the experimental and computational methods developed by the Human T2T Consortium to determine the complete sequences for the sex chromosomes of our closest living relatives -- great apes."

The team produced complete sex chromosome sequences for five species of great apes -- chimpanzee, bonobo, gorilla, Bornean orangutan and Sumatran orangutan, which comprise most great ape species living today -- as well as a lesser ape, siamang. They generated sequences for one individual of each species. The resulting reference genomes act as a map of genes and other chromosomal regions, which can help researchers sequence and assemble the genomes of other individuals of that species. Previous sex chromosome sequences for these species were incomplete or -- for the Bornean orangutan and siamang -- did not exist.

"The Y chromosome has been challenging to sequence because it contains many repetitive regions, and, because traditional short-read sequencing technology decodes sequences in short bursts, it is difficult to put the resulting segments in the correct order," said Karol Pál, postdoctoral researcher at Penn State and a co-first author of the study. "T2T methods use long-read sequencing technologies that overcome this challenge. Combined with advances in computational analysis, on which we collaborated with Adam Phillippy's group at the NHGRI, this allowed us to completely resolve repetitive regions that were previously difficult to sequence and assemble. By comparing the X and Y chromosomes to each other and among species, including to the previously generated human T2T sequences of the X and the Y, we learned many new things about their evolution."

High variability on the Y chromosome

"Sex chromosomes started like any other chromosome pair, but the Y has been unique in accumulating many deletions, other mutations and repetitive elements because it does not exchange genetic information with other chromosomes over most of its length," said Makova, who is also the director of the Center for Medical Genomics at Penn State.

As a result, across the six ape species, the research team found that the Y chromosome was much more variable than the X over a variety of characteristics, including size. Among the studied apes, the X chromosome ranges in size from 154 million letters of the ACTG alphabet -- representing the nucleotides that make up DNA -- in chimpanzee and human to 178 million letters in gorilla. In contrast, the Y chromosome ranges from 30 million DNA letters in siamang to 68 million letters in Sumatran orangutan.

The amount of DNA sequence shared between species was also more variable on the Y. For example, about 98% of the X chromosome aligns between human and chimpanzee, but only about a third of the Y aligns between them. The researchers found that this is in part because the Y chromosome is more likely to be rearranged or have portions of its genetic material duplicated.

Additionally, the percentage of the chromosome occupied by sequences that are repeated is highly variable on the Y. Whereas, depending on the species, 62% to 66% of the X chromosomes are occupied by repetitive elements, 71% to 85% of the Y chromosomes are occupied by them. These percentages are higher on both the X and the Y than in other chromosomes in the human genome.

How the Y has survived

"We found the ape Y to be shrinking, accumulating many mutations and repeats, and losing genes," Makova said. "So why hasn't the Y chromosome disappeared, as some previous hypotheses suggested? In collaboration with Sergei Kosakovsky Pond from Temple University and others, we found that the Y chromosome still has a number of genes evolving under purifying selection -- a type of natural selection that keeps gene sequences intact. Many of these genes are important for spermatogenesis. This means that the Y chromosome is unlikely to disappear any time soon."

The researchers found that many genes on the Y chromosome seem to use two strategies to survive. The first takes advantage of genetic redundancy -- the presence of multiple copies of the same gene on a chromosome -- so that intact copies of the gene can compensate for copies that might acquire mutations. The team quantified this genetic redundancy by completing the landscape of multi-copy gene families on ape sex chromosomes for the first time.

The second survival strategy takes advantage of palindromes, where the sequence of letters in the DNA alphabet is followed by the same, but inverted sequence, for example, ACTG-GTCA. When located within a palindrome, genes benefit from the palindrome's ability to correct mutations.

"We found that the Y chromosome can exchange genetic information with itself between the repeated sequences of the two palindrome arms, which fold so that the inverted sequences align," Pál said. "When two copies of the same gene are located within palindromes, and one copy is hit by a mutation, the mutation can be rescued by the genetic exchange with another copy. This can compensate for the Y's lack of genetic information exchange with the other chromosomes."

The research team obtained the complete sequences of palindromes on ape sex chromosomes also for the first time, as they were previously difficult to sequence and study. They found that palindromes are particularly abundant and long on the ape Y chromosome, yet they are usually only shared among closely related species.

In collaboration with Michael Schatz and his team at Johns Hopkins University, the researchers also studied the sex chromosomes of 129 individual gorillas and chimpanzees to better understand the genetic variation within each species and search for evidence of natural selection and other evolutionary forces acting on them.

"We obtained substantial new information from previously studied gorilla and chimpanzee individuals by aligning their sex chromosome sequencing reads to our new reference sequences," said Zachary Szpiech, assistant professor of biology at Penn State and an author of the paper. "While increasing the sample size in the future will be very helpful to improve our ability to detect signatures of different evolutionary forces, this can be ethically and logistically challenging when working with endangered species, so it is critical that we can get the most out of the data we do have."

The researchers explored a variety of factors that could explain variation on the Y chromosome within gorillas and within chimpanzees, and this analysis revealed additional signatures of purifying selection on the Y. This confirms the role of this type of natural selection on the Y, as was discovered in their previous analyses of genes.

"The powerful combination of bioinformatic techniques and evolutionary analyses that we used allows us to better explain the evolutionary processes acting on sex chromosomes in our closest living relatives, great apes," said Christian Huber, assistant professor of biology at Penn State and an author of the paper. "Additionally, the reference genomes we produced will be instrumental for future studies of primate evolution and human diseases."

In addition to Makova, Pál, Szpiech and Huber, the research team at Penn State includes Kaivan Kamali, computational scientist in the departments of biology and of biochemistry and molecular biology; Troy LaPolice, graduate student in bioinformatics and genomics; Paul Medvedev, professor of computer science and engineering and of biochemistry and molecular biology; Sweetalana, research assistant in the department of biology; Huiqing Zeng, research technologist in biology; Xinru Zhang, graduate student in bioinformatics and genomics; Robert Harris, assistant research professor of biology, now retired; Barbara McGrath, associate research professor of biology, now retired; and Sarah Craig, associate research professor of biology, currently a program officer at the National Institutes of Health. The co-authors also included Penn State alumni Monika Cechova, currently a postdoctoral fellow at the University of California Santa Cruz, and Melissa Wilson, currently an associate professor at Arizona State University.

In addition to Makova, the team was co-led by co-corresponding study authors Adam Phillippy, senior investigator at NHGRI, and Evan Eichler, professor of Genome Sciences at the University of Washington. A full list of authors for this paper is available here.

Funding from the National Institutes of Health supported this research.

Complete X and Y chromosome sequences of living great ape species determined (2024)

FAQs

Do apes have X and Y chromosomes? ›

While great-ape X chromosomes are highly conserved, their Y chromosomes, reflecting the general lability and degeneration of this male-specific part of the genome since its early mammalian origin, have evolved rapidly both between and within species.

What is determined genetically by the combination of X and Y chromosomes? ›

The X and Y chromosomes, also known as the sex chromosomes, determine the biological sex of an individual: females inherit an X chromosome from the father for a XX genotype, while males inherit a Y chromosome from the father for a XY genotype (mothers only pass on X chromosomes).

How many chromosomes does a great ape have? ›

In other words, humans and chimps have DNA sequences that are greater than 98 percent similar. While the genetic similarity between human and ape strengthened Darwin's theory, a significant, unexplained discrepancy remained. While great apes all have 48 chromosomes (24 pairs), humans have only 46 (23 pairs).

What determines if an organism will be male or female either X or Y? ›

If the egg receives another X chromosome from the sperm, the resulting individual is XX, forms ovaries, and is female; if the egg receives a Y chromosome from the sperm, the individual is XY, forms testes, and is male. The Y chromosome carries a gene that encodes a testis-determining factor.

What species have X and Y chromosomes? ›

The XY sex-determination system is a sex-determination system used to classify many mammals, including humans, some insects (Drosophila), some snakes, some fish (guppies), and some plants (Ginkgo tree).

Which gender has X and Y chromosomes? ›

Each person normally has one pair of sex chromosomes in each cell. The Y chromosome is present in males, who have one X and one Y chromosome, while females have two X chromosomes. Identifying genes on each chromosome is an active area of genetic research.

What are the combinations of X and Y chromosomes? ›

The sub-categories that exist within X & Y Chromosomal Variations are identified by names that include 47, XXY (Klinefelter syndrome), 47, XYY (Jacob's syndrome), 47, XXX (Triple X), 49, XXXXY, Tetrasomy X, Pentasomy X, 49, XXXXXX, and 48, XXXY.

What chromosomes determine your biological X and Y? ›

Sex Determination in Mammals

Normally, cells from females contain two X chromosomes, and cells from males contain an X and a Y chromosome. Occasionally, individuals are born with sex chromosome aneuploidies, and the sex of these individuals is always determined by the absence or presence of a Y chromosome.

Which parent gives the X and Y chromosome? ›

Females always pass an X chromosome onto their offspring. If the father passes on an X chromosome, the baby will be genetically female, and if the father passes on a Y chromosome, the baby will be genetically male.

How much DNA do we share with great apes? ›

But for a clear understanding of how closely they are related, scientists compare their DNA, an essential molecule that's the instruction manual for building each species. Humans and chimps share a surprising 98.8 percent of their DNA.

Why do great apes have 48 chromosomes? ›

Humans have 46 chromosomes, whereas chimpanzee, gorilla, and orangutan have 48. This major karyotypic difference was caused by the fusion of two ancestral chromosomes to form human chromosome 2 and subsequent inactivation of one of the two original centromeres (Yunis and Prakash 1982).

Can great apes hybridize? ›

Sister great ape species within the same genus can interbreed and produce fertile offspring in zoos, but not in the wild where their ranges generally do not overlap.

What determines if a chromosome is X or Y? ›

At conception, the mother gives an X chromosome to the child, and the father may contribute an X or a Y. The chromosome from the father determines if the baby is female or male. In most cases, a child is born as a male or female according to their chromosomes.

What does the Y chromosome determine? ›

But the human Y chromosome, at the same time, plays a central role in human biology. The presence or absence of this chromosome determines gonadal sex. Thus, mammalian embryos with a Y chromosome develop testes, while those without it develop ovaries (Polani [1]).

What are the chromosomes X and Y determine the individual's gender and are therefore called? ›

People usually have 46 chromosomes in each cell. Two of the 46 chromosomes, known as X and Y, are called sex chromosomes because they help determine whether a person will develop male or female reproductive structures.

Do pigs have X and Y chromosomes? ›

Each pig has about 70 billions cells, each containing 38 chromosomes in the nucleus of each cell. Two of the chromosomes, called sex chromosomes, mostly dictate the sex of the pig: two X-chromosomes result in a female pig while one X-chromosome and one Y-chromosome result in a male.

Do apes have gender? ›

Gender diversity exists among primates as well. Not all animals 'act' like the biological sex they were born with. “Donna, for example, was a chimpanzee that was born with female physical characteristics, yet Donna displayed more masculine behaviour.

Which animal has only X chromosome? ›

In fruit flies, males have only one X chromosome, while females have two X chromosomes. However, birds have a completely different set of chromosomes.

Can a human have both X and Y chromosomes? ›

The person has both ovarian and testicular tissue. This may be in the same gonad (an ovotestis), or the person might have 1 ovary and 1 testis. The person may have XX chromosomes, XY chromosomes, or both. The external genitals may be ambiguous or may appear to be female or male.

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