First complete chromosome sequences generated from non-human primates
New research funded by the National Institutes of Health has generated the first complete chromosome sequences from non-human primates. These sequences highlight variations between the Y chromosomes of different species, offering insights into our evolution.
The focus of the study was on the X and Y chromosomes, which play crucial roles in sexual development, fertility, and numerous other biological functions. They sequenced chromosomes from five great ape species— chimpanzee, bonobo, gorilla, Bornean orangutan, and Sumatran orangutan— alongside a more distantly related primate species, the siamang gibbon.
“These chromosome sequences add a significant amount of new information,” remarked Brandon Pickett, Ph.D., a postdoctoral fellow at the National Human Genome Research Institute (NHGRI), in a statement. “Only the chimpanzee genome sequence was fairly complete before this, but even that still had large gaps, especially in regions of repetitive DNA,” he added.
Repetitive DNA in chromosome complexity
Their study revealed that a substantial portion of both the X and Y chromosomes consists of repetitive DNA sequences— 62 to 66% for the X chromosomes and 75 to 82% for the Y chromosomes. These repetitive sequences, historically challenging to characterize, have only recently become accessible due to advancements in DNA sequencing technologies.
The researchers found an alignment of over 90% when comparing ape X chromosome sequences to human X chromosomes. This indicates stability over millions of years of evolution. In contrast, only 14% to 27% of ape Y chromosome sequences aligned with the human Y chromosome.
“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.”
One notable difference among the primate Y chromosomes is their length. For instance, the Sumatran orangutan’s Y chromosome is twice as long as that of the gibbon. Variations in the number and types of DNA repeats contribute significantly to these differences in chromosome lengths.
DNA palindromes and satellites
Among the repetitive DNA sequences are palindromes, playing a crucial role. These palindromes are sequences with inverted DNA repeats, similar to language palindromes like “racecar.”
In primate chromosomes, these palindromes, which can exceed 100,000 letters, often contain multiple gene copies. This redundancy, the team believes, protects essential genes, especially on the Y chromosome, which typically exists as a single copy per cell. “Having these genes in palindromes is like keeping a backup copy,” explained Adam Phillippy, Ph.D., a senior investigator at NHGRI and senior author of the study.
Within these palindromes, the team examined several gene groups vital for sperm production and, consequently, fertility. While palindromes were found across all studied primate Y chromosomes, the specific sequences and genes they contained varied significantly between species.
“There may be even more variation we’re not yet seeing,” Dr. Phillippy noted. “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.”
Additionally, the study also identified previously unknown species-specific DNA satellite sequences essential for functions such as organization during cell division.
Implications for evolution
The team’s findings present new avenues for understanding the evolution of great apes and humans. “Similar to our other findings about the Y chromosome, we can see that the centromere of the Y chromosome is highly dynamic,” highlighted Dr. Makova. Centromeres are special regions of chromosomes that play a crucial role during cell division.
According to the team, the rapid evolution of the Y chromosome can be attributed to factors, including male mutation bias. Sperm production involves more DNA replication than egg production. This implies a chance of the DNA sequence changing with each replication, particularly impactful for the Y chromosome.
Additionally, many of these great ape species are endangered, and understanding their genetic makeup can inform strategies to protect and preserve these species.
“Not only can we learn about human evolution from these sequences,” emphasized Dr. Makova. “We can apply what we know about their genomes and human genomes to better understand the biology and reproduction of these endangered species.”
Source: Interesting Engineering
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First complete chromosome sequences generated from non-human primates