Bioscience Methods 2025, Vol.16, No.3, 137-153 http://bioscipublisher.com/index.php/bm 137 Review and Progress Open Access Mitochondrial Genome Evolution of Abalone and Its Applications in Species Identification Chengmin Sun1, RudiMai 2 1 Tropical Marine Fisheries Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China 2 Tropical Biological Resources Research Center, Hainan Institute of Tropical Agricultural Resources, Sanya, 572025, Hainan, China Corresponding email: rudi.mai@hitar.org Bioscience Methods, 2025, Vol.16, No.3 doi: 10.5376/bm.2025.16.0013 Received: 21 Mar., 2025 Accepted: 29 Apr., 2025 Published: 19 May, 2025 Copyright © 2025 Sun and Mai, 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: Sun C.M., and Mai R.D., 2025, Mitochondrial genome evolution of abalone and its applications in species identification, Bioscience Methods, 16(3): 137-153 (doi: 10.5376/bm.2025.16.0013) Abstract The genus Haliotis includes a variety of marine shellfish with important economic and ecological values. In recent years, the mitochondrial genome has received extensive attention in the study of abalone systematic classification and species identification due to its unique advantages. This study systematically sorted out the structural characteristics of the abalone mitochondrial genome, the genetic variation pattern and the evolutionary relationship between different species, focusing on the analysis of the role of SNP and non-synonymous mutations in adaptive evolution. Through the construction of a whole-genome phylogenetic tree, the lineage differentiation and geographical isolation correlation within the genus Haliotis were revealed, and the application potential of mitochondrial DNA markers (such as COI gene) in rapid species identification and traceability detection was evaluated. Combined with case analysis, the mitochondrial variation characteristics of abalone species in the southeast coast of China were compared, the genetic differences between introduced populations and local populations were evaluated, and the disputes over the classification of abalone in Japan, Australia and East Asia were discussed. The study shows that the evolutionary characteristics of the abalone mitochondrial genome are of great value for species identification, but different methods have their own advantages and limitations. This study aims to provide a basis for the systematic classification of the abalone genus, and to provide theoretical support for the scientific management of my country's abalone germplasm resources, the protection of genetic diversity and sustainable utilization, so as to improve the quality of abalone seed industry and ensure the ecological security of marine fisheries. Keywords Abalone; Mitochondrial genome; Phylogeny; DNA barcode; Species identification 1 Introduction The genus Haliotis is a large gastropod mollusk with great economic and ecological value in the ocean. Its meat is tender and nutritious, making it a popular seafood delicacy. It is farmed and harvested along the coasts of the world. According to statistics, more than 50 abalone species have been reported worldwide, and about 7 species are distributed along the coast of China, mainly including the wrinkled disc abalone (Haliotis discus hannai) and the variegated abalone (H. diversicolor), showing rich species diversity (Chen et al., 2016). Abalone not only has important fishery and aquaculture value, but is also an ideal material for studying the adaptive evolution and biogeographic distribution of shellfish. Some large abalone species have been listed as endangered species due to overfishing and resource decline. It is urgent to protect their genetic diversity. In recent years, China's abalone farming industry has developed rapidly and production has increased significantly. In 2018, production increased by about 14.5 times compared with 2003 (You, 2023). With the expansion of the abalone industry and the increase in cross-regional introduction activities, it is increasingly important to quickly and accurately identify abalone species and germplasm. This is not only related to the selection and breeding of fine varieties and aquaculture management, but also has practical significance for preventing species confusion, maintaining market order and protecting wild resources. Due to its special genetic characteristics, mitochondrial DNA has been widely used in the classification and evolution of marine invertebrates. Compared with the nuclear genome, the mitochondrial genome has a compact structure (no introns), uniparental inheritance, and a small effective size, making it easy to obtain the full sequence, so it is often used to infer molecular phylogenetic relationships and species identification. The mitochondrial genome of mollusks such as abalone usually contains 13 protein-coding genes, 2 rRNA genes, and 22 tRNA genes,
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