International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 38 genome size of the shrimp, such as the vannamei shrimp, has not yet reached the 2.45 Gb measured by flow cytometry (Fu et al., 2024). However, these achievements are enough to lay a more solid foundation for in-depth research on the genetic mechanism of shrimp. On the other hand, there have been some progress in freshwater shrimp, such as Macrobrachium rosenbergii, whose chromosome-level genome was finally released in 2024 (Zheng et al., 2024). Now, more than 20 decapod species have completed genome drafts, and the shrimp genome database is much richer than before. With these data, researchers can compare the genomes of various species to find out which genes are shared by everyone and which are unique, so as to further explore the genetic clues behind shrimp evolution. 4 Application of Comparative Genomics in the Study of Decapod Shrimp Evolution 4.1 Reconstruction of phylogenetic and phylogenetic relationships The emergence of comparative genomics has provided new ideas for solving many mysteries in evolutionary history. Especially in recent years, with the continuous accumulation of shrimp genome and transcriptome data, researchers can use hundreds of single-copy orthologous genes to perform phylogenetic analysis, and the resolution of phylogenetic trees is much higher than in the past. For example, the shrimp phylogenetic tree built by Wolfe et al. (2019) using hundreds of genes strongly supports the monophyly of lineages such as true shrimp, prawns, and crayfish. In the past, the practice of relying only on mitochondrial genes or a few nuclear genes often struggled to distinguish the relationship between closely related species. Now, with the use of whole genome data, the divergence time can be more clearly inferred, and the evolutionary timeline drawn is more reliable. Of course, comparative genomics not only helps to clarify phylogenetic relationships, but also can correct old classification systems. For example, mud shrimps were not accurately divided in the past, but later confirmed that they should be split into two independent lineages based on genomic evidence (Lin et al., 2012). In general, large-scale genome comparisons have indeed brought shrimp phylogenetic research to a new level. 4.2 Genome evolution patterns and key events In fact, the genomes of different shrimps have undergone many special changes during their evolution. By comparing the genomes of multiple species, Yuan et al. (2021b) found that simple repeat sequences (SSRs) in the shrimp genome have expanded on a large scale, which is the first time they have been seen in crustaceans. This expansion is likely related to some special genome evolution mechanisms. In addition, there are differences in genome size and the number of repetitive elements between different species. Studies such as Rutz et al. (2023) reveal which factors are driving genome expansion or contraction. Not only between aquatic species, researchers have also compared the genomes of aquatic and semi-terrestrial crustaceans. For example, Veldsman et al. (2021) found that genes related to osmotic regulation and nitrogen waste excretion have undergone significant changes in some groups living close to land. These comparisons help us better understand how shrimps constantly adjust their genomes in different environments. 4.3 Adaptive traits and ecological adaptation mechanisms The ability of shrimp to adapt to the environment is far more complicated than imagined. From deep-sea hydrothermal vents to extreme salinity, to freshwater and even land, they have evolved many special traits in various environments. Comparative genomics has been very useful in this regard. For example, by comparing shrimps living in hydrothermal environments with closely related species, we can find some genes related to chemosymbiosis and high temperature resistance (Yuan et al., 2020), such as enzymes that can detoxify sulfides. For example, by comparing the genomes of freshwater crayfish and marine shrimp, we can find that freshwater species often have signs of expansion or positive selection in genes related to osmotic pressure regulation (Wang et al., 2022), indicating that these genes are important for their adaptation to low-salinity environments. Even the evolution of social behavior can be explored through comparative genomics, such as analyzing the genomic differences between social pistol shrimp and solitary closely related species to find genes that may be related to social behavior. In short, comparative genomics has now become one of the core tools for understanding the evolutionary diversity and ecological adaptability of shrimp.
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