International Journal of Marine Science, 2025, Vol.15, No.1, 1-14 http://www.aquapublisher.com/index.php/ijms 1 Research Report Open Access Whole-Genome Analysis of Abalone Reveals Phylogenetic Relationships and Adaptive Evolution Mechanisms Xuelian Jiang1,ManmanLi 2 1 Institute of Life Science, Jiyang College of Zhejiang A&F University, Zhuji, 311800, Zhejiang, China 2 Hainan Institute of Biotechnology, Haikou, 570206, Hainan, China Corresponding author: 502684238@qq.com International Journal of Marine Science, 2025, Vol.15, No.1, doi: 10.5376/ijms.2025.15.0001 Received: 09 Dec., 2024 Accepted: 14 Jan., 2025 Published: 23 Jan., 2025 Copyright © 2025 Jiang and Li, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Jiang X.L., and Li M.M., 2025, Whole-genome analysis of abalone reveals phylogenetic relationships and adaptive evolution mechanisms, International Journal of Marine Science, 15(1): 1-14 (doi: 10.5376/ijms.2025.15.0001) Abstract Abalone (Haliotis) molluscs play an important role in marine biodiversity and aquaculture, but their phylogenetic relationships and adaptive evolutionary mechanisms have not been fully elucidated. Whole genome sequencing in recent years has provided a new opportunity to study the systematic evolution and environmental adaptation of abalone. In this study, by comparing the whole genome data of multiple abalone species, we reconstructed the phylogenetic tree of the genus Abalone, estimated the divergence time, and analyzed the evolutionary characteristics of genome structure and function. The results showed that the abalone genome size ranged from 1.2 Gb to 1.8 Gb, encoding approximately 20 000 to 30 000 genes, with a repetitive sequence ratio of nearly 50%. Positively selected genes related to temperature, salinity, and immunity were identified, as well as the expansion of specific gene families involved in shell formation and metabolic pathways. These adaptive genomic changes may explain the adaptation of abalone to different environments such as high latitudes and tropical waters. Taking the representative species of Japanese abalone, African abalone and Australian green abalone as examples, this study deeply analyzed the adaptive characteristics in their genomes, including cold-adapted immune genes, multiple heat-resistant genes and shell morphology-related selection signals, and discussed the application prospects of abalone whole genome research in germplasm protection, molecular breeding and stress resistance breeding. This study provides a new perspective at the genome level for understanding the phylogeny and environmental adaptation of abalone, and also provides a scientific basis for abalone resource protection and genetic improvement. Keywords Abalone; Whole genome; Phylogeny; Adaptive evolution; Genomic breeding 1 Introduction The genus Haliotis includes more than 50 species of marine gastropod mollusks, which are distributed in tropical and temperate coastal areas around the world except the northern Atlantic Ocean. Abalone feeds on large algae in a benthic lifestyle and plays an important role in maintaining the balance of algae beds in marine ecosystems (Barkan et al., 2024). At the same time, abalone has been a famous "sea treasure" since ancient times. It is highly praised for its delicious meat and high nutritional value and is known as one of the "eight treasures of seafood". Due to its high economic value, abalone has also become an important farmed shellfish in the world. Especially in China, the abalone farming industry has developed rapidly in recent decades: as of 2020, China's annual abalone production is about 203 500 tons, accounting for more than 85% of the global abalone farming production. Among them, the main species is the wrinkled disc abalone (Haliotis discus hannai), which occupies the leading position in aquaculture production. While large-scale farming meets market demand, it also puts higher requirements on abalone resource protection and industry sustainability (Zhang et al., 2022). In recent years, factors such as illegal fishing, habitat destruction and warming sea water caused by climate change have caused a sharp decline in many wild abalone populations. About 20 of the world's 54 abalone species are at risk of extinction. Although abalone is important, both in terms of classification and breeding, people do not know enough about its evolutionary relationships, and most previous studies rely on appearance and mitochondrial gene analysis. These methods are controversial and not accurate enough. The relationships between abalone species obtained by different studies are not the same, and the classification of some abalone is still uncertain. Species such as the
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