International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 3 2.2 Gene content, repetitive elements, and unique genomic features The abalone genome has a high gene content and relatively low gene density, reflecting its large genome size and rich non-coding regions. Compared with model mollusks (such as golden snails and oysters), many genes in the abalone genome have multiple copies or gene family expansion. For example, the Pacific abalone Haliotis discus has a very developed aquaporin gene family, with a total of 18 members identified, more than double the number of AQP family members in most mollusks (Jia et al., 2022; Zhao and Wu, 2024). These aquaporin genes may give abalone stronger water regulation ability under osmotic and temperature stress through gene duplication and functional differentiation. For another example, the matrix protein genes related to abalone shell formation show rich innovation and diversity. Transcriptome and proteome studies have shown that the mantle secretory protein (i.e., shell matrix protein) collections of different abalone species are significantly different, including a large number of genus-specific new genes and special repetitive domains (Xin et al., 2017). These low-complexity repeat sequences (RLCDs) are often generated through mechanisms such as slipped replication and gene recombination, thus promoting the expansion and diversification of the shell matrix protein family. In addition to the expansion of functional genes, there are also some unique repeat sequences in the abalone genome. For example, some abalone-specific transposable elements are only found in abalone and its closely related species, suggesting that they may play a unique role in the evolution of the abalone genome. It is worth noting that the genomic microsatellites and scattered repeat sequences of abalone are very rich. This provides material for population genetics and molecular marker screening, but also increases the difficulty of gene assembly and sequencing. With the application of third-generation sequencing and Hi-C technology, these complex regions can be more completely analyzed in the future, so as to better explore the potential functional elements in the abalone genome. 2.3 Evolutionary conservation and divergence in mollusks Comparative genomic studies have shown that the abalone genome has retained some common characteristics in mollusks and has also evolved its own uniqueness. In terms of conservation, abalone shares a large number of ancient developmental genes and metabolic pathway genes with other mollusks (such as bivalve oysters, stone snails, etc.). For example, core genes related to shell mineralization, neural regulation, and energy metabolism are highly conserved among all groups of molluscs. This reflects that as an ancient evolutionary lineage, molluscs have a relatively stable genetic blueprint for basic life processes. However, there are significant differences between abalone and other molluscs in terms of genome size, gene family, and repetitive sequences. The bivalve oyster genome (~560 Mb) is much smaller than that of abalone, probably because it has undergone genome contraction and lower repetitive sequence content. However, the genome of some gastropods, such as the golden apple snail (>2 Gb), is larger than that of abalone, indicating that the genomes of gastropods with different ecological habits have experienced different expansion histories. Abalone also differs from other marine shellfish in terms of immune and stress-related genes. For example, the number of Toll-like receptor (TLR) families encoded in the abalone genome varies greatly among different species: the wrinkled abalone has 29 TLR genes, while the red abalone has 33 and the green abalone has only 16. This difference may reflect the different evolutionary strategies of each species to cope with their own pathogenic pressures. Compared with bivalves, gastropods such as abalone have a more complex neuroendocrine regulation system, which is reflected in the expansion of neuropeptide and hormone receptor gene families. For example, dozens of new neuropeptide precursor and receptor genes have been identified in the green abalone genome, which may play an important role in regulating reproduction and metabolism. The abalone genome has both commonalities and individuality with other mollusks. 3 Phylogenetic Reconstruction Using Whole-Genome Data 3.1 Phylogenetic tree inference across abalone species Tshilate et al. (2023) collected high-quality genome sequence data of multiple representative species of the genus Abalone (includingH. discus, H. japonicus, H. variegated, H. red, H. black, H. green, etc.), and used phylogenetic genomics methods to reconstruct their phylogenetic relationships (Figure 1). By selecting tandem orthologous single-copy genes, this study obtained spliced sequences containing about hundreds of conserved proteins, and
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