International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 2 nine-hole abalone have different views in molecular research, and traditional classification results do not match genetic data (Agius et al., 2024). Past genetic research has mainly focused on mitochondrial genes or a few nuclear genes, and the research content is relatively limited. Only in recent years have a few abalone genomes been measured, but most of them are only rough versions and are not detailed enough. These genomic data are far from enough, which affects our in-depth understanding of abalone genes and functions. For example, the first abalone genome was a draft version of the wrinkled abalone, which was not released until 2017. Later, the red abalone, black abalone, etc. also had genomes, but some tropical abalone and variegated abalone species have not yet had relevant data. Due to the lack of complete genetic information, it is also difficult for us to figure out how abalone adapts to different environments, such as temperature, salinity and pathogens. At present, the improvement of abalone's stress resistance and growth traits mainly relies on traditional breeding methods, and the genes and molecular mechanisms related to these traits have not been figured out. Now with the development of high-throughput sequencing technology, we have the hope of using the whole genome to study the evolutionary relationship of the abalone genus (Pu et al., 2020; Wang et al., 2023). By comparing the complete genomes of different abalone species, we can draw a clearer phylogenetic tree and find important genes related to environmental adaptation. However, research in this area is still in its infancy, and further improvement is needed in species selection and genome quality. This study will use abalone whole genome data to systematically analyze the phylogenetic relationships and adaptive evolutionary mechanisms of abalone species, integrate the genomes of multiple abalone species published in the past five years (including Abalone discus, Abalone japonensis, Abalone rubrum, Abalone nigromaculata, Abalone occidentalis, etc.), conduct comparative analysis of their genomic structural characteristics, and construct a phylogenetic tree of abalone based on high-confidence single-copy orthologous genes, explore the evolutionary history and geographical diffusion process of abalone, identify genes and gene families that show rapid evolution in different environments, including candidate genes related to temperature, salinity adaptation and immune defense, as well as gene expansion related to shell mineralization, growth metabolism, and select three representative abalone species as cases for in-depth analysis. This study analyzes abalone phylogeny and adaptive evolution at the whole genome scale, providing an important reference for future functional genomics research and molecular breeding practices. 2 Genome Architecture and Evolutionary Characteristics 2.1 Overview of abalone genome size and structure The diploid chromosome number of abalone species is usually 2n=36 or 32, corresponding to 18 or 16 pairs of haploid chromosomes. The sequenced abalone genome size is in the range of about 1.2 Gb~1.8 Gb, with the characteristics of a medium genome size. For example, the size of the assembled genome of Abalone discus is about 1.86 Gb, with a GC content of about 40.5%; the draft genome of Abalone africanus is about 1.50 Gb; the genome of Abalone cracherodii is about 1.71 Gb; the genome of Abalone cracherodii is relatively small, about 1.2 Gb. Abalone genomes are generally high in proportion to repetitive sequences and transposons, which is one of the main reasons for the large size of mollusc genomes (Dale-Kuys et al., 2017). It is reported that the total amount of repetitive sequences in the genome of Abalone discus is more than 40%, of which scattered repetitive elements (such as LINE, class I and class II transposons) are the main ones. In terms of the number of predicted genes, the species are not much different, generally containing more than 20 000 coding genes. For example, the predicted genes of Haliotis discus are about 23 400; the green abalone genome has annotated about 27,700 protein-coding genes; the number of genes in the red abalone and black abalone genomes is also between 23,000 and 25 000. In terms of genome assembly quality, the latest research has improved from the initial short-read fragment assembly to chromosome-level assembly. For example, the tropical abalone H. asinina recently obtained the first high-quality genome at the chromosome level, with a total of 18 assembled chromosomes, which is consistent with the karyotype. The abalone genome structure has a similar composition framework to other gastropod mollusks, but also shows some family-specific characteristics, such as large-scale genome duplications, low GC content, and gene cluster distribution (Barkan et al., 2024). These characteristics may be related to the unique development and metabolism of mollusks, providing background information for subsequent in-depth research.
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