Oldest vertebrate sex chromosomes discovered —X chromosomes in sharks and rays have retained common gene set for 300 million years

A research group consisting of Graduate Student Taiki Niwa from SOKENDAI (the Graduate University for Advanced Studies), Professor Shigehiro Kuraku from the Molecular Life History Laboratory at the National Institute of Genetics, Associate Professor Yoshinobu Uno from the Graduate School of Technology, Industrial and Social Sciences at Tokushima University, Research Advisor Masaru Nakamura at the Okinawa Churashima Foundation Research Institute, Research Associate Wataru Takagi from the Atmosphere and Ocean Research Institute at the University of Tokyo, and multiple aquariums announced that they conducted research by comparing the genome sequences of cartilaginous fishes. They have revealed that based on the comparisons, the X chromosomes of sharks and rays maintain a common gene set, while Y chromosomes have lost most of their genes, and that these sex chromosomes have likely been maintained for approximately 300 million years. This shows that sharks and rays have a different mechanism for sex determination from other vertebrates. The results were published in Proceedings of the National Academy of Sciences USA (PNAS) on July 23.

Vertebrates have diverse sex determination mechanisms. In humans, sex is determined by inheritance from both parents, with male determination occurring when the Y chromosome is inherited from the father. The origins of sex chromosomes in mammals and birds are relatively ancient, dating back over 100 million years, with significant size differences between the pair. In contrast, most fish (ray-finned fish) have sex chromosomes with newer origins, with little size difference between the pair. Therefore, an evolutionary pathway has been proposed where the one of sex chromosomes become shorter over generations and the lost portions are replaced by new ones.

Cartilaginous fish, including sharks and rays, are phylogenetically distant from other vertebrate lineages and have undergone unique evolution, with their sex determination mechanisms being largely unknown. Karyotype analysis through microscopic observation suggested that some cartilaginous fish species determine sex through XX/XY-type sex chromosomes, but their evolutionary pathway remained unclear.

Therefore, the research group created chromosome-level whole genome sequences for the brownbanded bamboo shark and cloudy catshark. By utilizing recently published whole genome sequences of other species, they identified and compared the genome sequences of sex chromosomes from multiple species.

As a result, they revealed that the X chromosomes of sharks and rays, which make up the majority of cartilaginous fish, maintain a common gene set. It became clear that the same sex chromosomes have likely been maintained from their common ancestor that existed approximately 300 million years ago to the present.

Sex chromosomes in mammals and birds are believed to have originated 100-200 million years ago, making cartilaginous fish sex chromosomes the oldest in origin among vertebrates.

Furthermore, in the brownbanded bamboo shark, the researchers successfully identified Y chromosome sequences by collecting only Y chromosome DNA and reading the base sequences. The number of genes on the Y chromosome was extremely low compared with the X chromosome.

Additionally, they continuously collected brownbanded bamboo shark eggs laid in aquariums and histologically observed the structure of gonads during the sex differentiation process. They found that in the brownbanded bamboo shark, the Y chromosome possessed only by males is rarely used, and sex is likely determined by gene expression according to the dosage ratio of X chromosomes, with females having two and males having one.

Kuraku commented: "Cartilaginous fish are often grouped together with bony fish like medaka and tuna as 'fish.' In this research, we were able to clarify based on genomic information that sharks and rays, which are cartilaginous fish, have a different sex determination mechanism from many of these other fish. Research targeting cartilaginous fish has faced high barriers in terms of body size, growth rate, and even sample acquisition, but through cooperation with multiple domestic aquariums with expertise in academic research, we were able to conduct this globally rare research using biological samples from multiple species. Research on reproductive mechanisms is an important field that can provide knowledge supporting ecosystem conservation and food security. We hope to continue supporting this from the perspective of genomic information analysis while pursuing understanding of diversity and evolution."

Journal Information
Publication: Proceedings of the National Academy of Sciences
Title: Sharks and rays have the oldest vertebrate sex chromosome with unique sex determination mechanisms
DOI: 10.1073/pnas.2513676122