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Deciphering the Y chromosome: Advances in Sequencing, Evolutionary Insights, and Biological Functions
The Y chromosome is one of the sex chromosomes of mammals that adopt the XY sex-determination system, and the presence or absence of the SRY gene it carries is critical in determining whether embryos of these animals develop into males. This literature review of ours synthesizes three research articles that provide a series of summaries and presentations on the nature of the Y chromosome and its evolution.

In exploring the nature of the Y chromosome, its evolutionary history, and the progress of its research, Bachtrog's (2013) review article provides insights and is a classic review of the history of Y chromosome research and the evolutionary history of the Y chromosome as we currently know it. The article describes how the Y chromosome evolved from an autosomal chromosome by analyzing the ancient Y chromosomes in primates and Drosophila, as well as the young Y chromosome in plants and the new Y chromosome in Drosophila.

The article by Bachtrog (2013) states that a central feature of Y chromosome evolution is the massive genetic decline. According to the article, the main reasons for the degradation of the Y chromosome include the cessation of recombination, sex-disparate mutations, male-restricted transmission, Muller's ratchet effect, and genetic hitchhiking, etc. Bachtrog (2013) states that the persistent absence of genes on the Y chromosome has led to the suggestion that the intrinsic idea that the Y chromosome will eventually disappear has been challenged, as recent research has shown that the Y chromosome will ultimately disappear. challenged by recent studies showing that empirical evidence of chromosome sequencing in fruit flies and primate Y chromosome gene content suggests that Y chromosome degeneration does not proceed in a simple linear fashion. Bachtrog (2013) concludes that the evolution of the sex chromosomes will benefit greatly from the genomics revolution, and that new sequencing technologies, particularly those that provide longer read lengths should be able to help us make new advances in this field. This statement was prescient, and the 2023 Telomere to Telomere (T2T) Consortium did succeed in obtaining the first complete sequence of the human Y chromosome utilizing ultra-long reads. (Rhie et al., 2023)

Bachtrog (2013) also points out the interesting phenomenon that the Y chromosome is completely extinct in a subset of organisms that are also XX/X0 sex-determined. The article writes that to eliminate the Y chromosome, organisms would have to evolve an alternative way of determining sex, and any genes required for male function would have to be converted to other chromosomes. the study by Terao et al. (2022) provides more examples and evidence for this, which we will discuss immediately below.

The study by Terao et al. (2022) is a relatively rare high-quality research article on mammals with XX/XO configurations, demonstrating a rare example of mammalian sex chromosome turnover. The article focuses on the SRY-deficient amami pinniped (Tokudaia osimensis), which lacks a Y chromosome, i.e., a y-chromosomally completely extinct animal as mentioned in the previous article by Bachtrog (2013). In most cases, the sex of a mammal is determined by the presence or absence of the SRY gene on the Y chromosome, but the amami pinniped is one of the exceptions in which the Y chromosome is extinct.

The researchers cut a small piece from the tip of the amami needle mouse's tail for sampling and then described in detail a comprehensive genomic analysis. The analysis showed that in male pinnipeds, a male-specific duplication of a Sox9 enhancer permits upregulation of Sox9 expression in the absence of SRY, and that Enh14 is a putative Sox9 enhancer. The authors concluded that this duplication appears to replace the function of SRY, defines a new Y chromosome for this species, and a new sex-determining mechanism appears to emerge. The enhancer is essential for testicular development in amphioxus pinnipeds and allows sox9 to function in the absence of SRY.

Terao et al., (2022) pointed out that the X chromosome is completely conserved in mammals, whereas the Y chromosome is significantly degraded due to the high mutation rate in the testis and the lack of recombination with the x chromosome, and that the amami pinniped mouse provides us with an extreme example, one that seems to show the correctness and keen foresight of Bachtrog's review article, where a complete deletion of the Y chromosome is found in A new Y chromosome is redefined in males after the deletion. This finding provides important insights into our understanding of how the Y chromosome has degenerated and remodeled during mammalian evolution.

Although the Y chromosome and the SRY genes it carries may not be indispensable in mammalian sex determination (Terao et al., 2022), and we have observed that the mammalian Y chromosome has been undergoing degradation for a long time (Bachtrog, 2013), sequencing the Y chromosome is still necessary, as Bachtrog suggests, because it is a key element in the evolution of mammals. However, as Bachtrog suggests, sequencing the Y chromosome is still necessary because it will clearly allow us to gain a deeper and more accurate understanding of the nature and evolution of the Y chromosome, and it will also help us to improve our methods for studying chromosomes with complex repeating structures, such as the human Y chromosome.

The study by Rhie et al., (2023), which assembled for the first time the human Y chromosome of the HG002 genome intact and named T2T-Y, is one of the latest scientific achievements of the Telomere-to-Telomere (T2T) consortium. This reference sequence contains 30 million more base pairs than GRCh38, while correcting several errors.

The assembly process for this project involved innovative sequencing and computational strategies, such as high-fidelity (HiFi) reads, and ultra-long reads, with extensive manual collation and multiple rounds of comparison and error correction.

In this project, gene annotation was performed using the RefSeq framework and the GENCODE framework in conjunction with Iso-seq transcriptome data. Rhie et al., (2023) performed comprehensive computational analyses and manual sorting based on new sequencing technologies to annotate repetitive elements in the Y chromosome, with special attention to noteworthy complex regions such as the heterochromatin Yq12 region, a thorough characterization of the Y chromosome concerning its structure and genetic content was performed, yielding the first complete human Y chromosome sequence.

The completion of T2T-Y was a milestone in human genomics. This study also facilitated improved variant detection and genomic analysis, especially for studies involving the Y chromosome, and collected important sequence information on the Y chromosome for subsequent determinations. All of these will be of significant help in our subsequent efforts to further understand the properties and evolutionary history of the Y chromosome, and to understand and predict its evolutionary trends.

To summarize, the work of Bachtrog (2013) delves into the evolutionary history of the Y chromosome, discussing the role of noteworthy factors such as Muller's ratchet effect and Genetic hitchhiking in the evolution of the Y chromosome declining phenotype. This review not only summarizes the complex process of how the Y chromosome evolved from a common autosomal chromosome, but also foresees how technological advances will drive new advances in sex chromosome research. The study by Terao et al. (2022) provides concrete examples of how sex determination in some species is achieved through other genetic mechanisms in the case of a complete deletion of the Y chromosome. The study by Rhie et al. (2023) assembled the first complete sequence of the human Y chromosome by using high-fidelity reads and ultra-long reads, an achievement that not only adds important information to the field of human genomics, but also provides new tools and methodologies for future research, mirroring the predictions of Bachtrog (2013).

Taken together, these studies emphasize the unique position of the Y chromosome in biology and genetics and its complex evolutionary history. The human Y chromosome is a chromosome with many complex repetitive structures that carry genes for sex determination and spermatogenesis. Y chromosomes have experienced significant gene loss in the past evolution, but this degradation is not necessarily linear and, based on our observations in species in which the Y chromosome has completely degraded, even if the Y chromosome were to become completely extinct, organisms would find alternative sex-determination systems to ensure that males would continue in the species. These findings also illustrate the importance of advances in sequencing technology for understanding the nature and evolution of the Y chromosome. In the future, with the development of new sequencing technologies, further deepening of human understanding of the nature and evolution of the Y chromosome is foreseeable.

Research Processes
After identifying our assessment topic, we first read the news article given on Moodle, and then we analyzed a series of press releases from reliable sources regarding the "complete sequencing of the Y chromosome", and finally concluded that the basic research on the complete sequencing of the Y chromosome is the most relevant to the nature and evolution of the Y chromosome. We then conducted a series of analyses around press releases from reliable sources related to "complete sequencing of the Y chromosome", and concluded that the basic research on the complete sequencing of the Y chromosome was the most relevant to the nature and evolution of the Y chromosome, along with our selected article from Rhie et al. We then oriented the general direction of our literature review around the nature and evolution of the Y chromosome, finding via Google Scholar an excellent REVIEW by Bachtrog, (2013) and an excellent study of an extreme case of Y chromosome degenerative evolution by Terao et al., (2022). These articles stood out when we sifted through the search engine mainly because of their fit with the topic and the reliability of the journals they were published.

In our literature review examining the nature and evolution of the Y chromosome, we analyzed a total of three key articles. Firstly, we have selected the review by Bachtrog (2013) to begin with, this is because it provides us with a comprehensive understanding of the evolutionary process of the Y chromosome. It delves into the many causes of degeneration and points out that the degeneration of the Y chromosome is likely to be nonlinear, but the article lacks a discussion of the important genes carried on the Y chromosome and the nature of the Y chromosome. Terao et al. (2022) enriched the discussion of Bachtrog's (2013) article on XX/X0 about sex determination by examining the amazo pinniped mouse, a species that is completely missing the Y chromosome, and deepened our understanding of the evolution of the Y chromosome. discussion of sex determination and deepens our understanding of the most extreme outcomes of persistent Y chromosome decline. Finally, Rhie et al. (2023) used cutting-edge sequencing technology to assemble the first complete sequence of the human Y chromosome, T2T-Y, marking a major breakthrough in sequencing technology. The article also begins with a brief introduction to the Y chromosome and its research history, which is very important for us to understand the nature, evolution and research history of the Y chromosome. However, the drawback is that the high level of specialization of the article makes it almost impossible for us to obtain any new results about the nature and evolution of the Y chromosome directly from the article, but only to analyze and understand the methodology adopted in the assembly process of T2T-Y. In summary, the articles we selected collectively present significant results on Y chromosome inheritance and evolution and our current knowledge of it, the authors and the journals in which they are published are well known in the academic community (authors have high H-indexes and journals have high impact factors), and the articles fit the topic very well, covering what we expected to discuss in a comprehensive, informative, and fruitful way. comprehensive, and excellent and fruitful content, which is the main reason for our selection of these articles.

In the course of our research, we mainly employed Google search and searching using Google Scholar, and adopted the strategy of following the cued press releases along the way. Generative Artificial Intelligence also contributed to this literature review-assisted reading and selection of articles.

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The article by Bachtrog (2013) highlights that the core feature of Y chromosome evolution is the significant decline of genes. It suggests that the main reasons for Y chromosome degradation include the cessation of recombination, sex-antagonistic mutations, male-limited transmission, Muller's ratchet effect, and genetic hitchhiking among others. Bachtrog (2013) notes that the continuous loss of genes on the Y chromosome challenges the prevailing belief that the Y chromosome will ultimately disappear. This is because recent studies, including chromosome sequencing in fruit flies and gene content analysis in primate Y chromosomes, indicate that Y chromosome degeneration does not proceed in a simple linear manner. Bachtrog (2013) concludes that the evolution of sex chromosomes will greatly benefit from a revolution in genomics. New sequencing technologies, especially those that offer longer read lengths, should enable us to make significant progress in this field. This prediction was prescient, as humans indeed utilized long-read sequencing technology to successfully obtain the first complete sequence of the human Y chromosome. (Rhie et al., 2023)

Bachtrog (2013) also points out an interesting phenomenon where the Y chromosome has completely disappeared in a subset of organisms, which are determined by an XX/X0 sex determination system. The article mentions that to completely eliminate the Y chromosome, organisms would inevitably evolve an alternative method of sex determination. The study by Terao et al. (2022) provides more examples and evidence for this, which will be discussed in detail in the following text.