International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 35 Review Article Open Access Evolutionary History of Decapod Shrimp Based on Comparative Genomics Fei Zhao, Jinni Wu Aquatic Biology Research Center, Cuixi Academy of Biotechnology, Zhuji, 311800, Zhejiang, China Corresponding author: jinni.wu@cuixi.org International Journal of Marine Science, 2025, Vol.15, No.1, doi: 10.5376/ijms.2025.15.0004 Received: 11 Jan., 2025 Accepted: 17 Feb., 2025 Published: 25 Feb., 2025 Copyright © 2025 Zhao and Wu, 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: Zhao F., and Wu J.N., 2025, Evolutionary history of decapod shrimp based on comparative genomics, International Journal of Marine Science, 15(1): 35-44 (doi: 10.5376/ijms.2025.15.0004) Abstract Decapod shrimps include shrimps, prawns, crayfishes and other groups, and have important research value in terms of biodiversity and evolutionary adaptation. In recent years, with the development of sequencing technology, a large number of shrimp genomes have been deciphered, providing unprecedented opportunities for revealing their evolutionary history based on comparative genomics. This article reviews the diversity and phylogeny of decapod shrimps and the latest progress in shrimp genome resources, focusing on the application of comparative genomics in clarifying the evolutionary relationships, key evolutionary events and environmental adaptation mechanisms of shrimps. For example, through genome comparative analysis, researchers found that the explosive expansion of simple repeat sequences (SSR) in the shrimp genome is closely related to its adaptive evolution; the genomes of eusocial species such as pistol shrimps have significantly expanded due to transposon accumulation. In a case study, we introduce how comparative genomic analysis of the Alpheidae family reveals the relationship between social behavior and genome evolution. Finally, the future direction of comparative genomics of decapod shrimps is prospected, such as deepening pan-genome construction and functional genome verification, to further reveal the full picture of shrimp evolutionary history. This article aims to show that comparative genomics has become an indispensable tool in the study of decapod shrimp evolution, providing a new perspective for understanding the evolution and adaptation of marine organisms. Keywords Decapod shrimp; Biodiversity; Comparative genomics; Evolutionary events; Environmental adaptation 1 Introduction Decapoda shrimps (hereinafter referred to as "shrimps") are an extremely diverse group of crustaceans, including shrimps, prawns, crayfish, krill and lobsters, and play a key role in marine and freshwater ecosystems (Rutz et al., 2023). There are more than 17 000 known decapoda species worldwide, a considerable proportion of which are shrimps (Wolfe et al., 2019). Shrimp not only plays an important role in ecology, but also is an important target of aquaculture and fisheries. For example, Pacific white shrimp (LitoPenaeus vannamei) has become the most produced crustacean cultured species in China in recent years. However, the research on high-level meta-taxonomy and phylogenetic relationships of shrimps has long been controversial. Traditional morphology and limited molecular markers make it difficult to fully analyze the complex evolutionary relationships of shrimps, and many key evolutionary issues remain unresolved. With the development of high-throughput sequencing technology, breakthroughs have been made in shrimp genomics research. Whole genome sequencing of a large number of shrimp species has been completed, laying the foundation for the use of comparative genomics to study the evolutionary history of shrimp (Zhang et al., 2019; Fu et al., 2024). Comparative genomics can reveal evolutionary signals that cannot be observed by traditional methods, such as whole genome duplication, gene family expansion, adaptive mutation, and convergent evolution patterns, by comparing gene sequences, genome structures, and functional elements of different species at the genome scale. In recent years, this method has been successfully applied to the phylogenetic reconstruction and adaptation mechanism research of decapod crustaceans, and has achieved rich results. This study aims to review the diversity and phylogenetic framework of decapod shrimps, sort out the main progress in the construction of shrimp genome resources in recent years, analyze the application results of comparative genomics in revealing important evolutionary events, environmental adaptation, and behavioral
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