International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 39 5 Key evolutionary Events Revealed by Comparative Genomics 5.1 Changes in genome size and expansion of repetitive sequences Among decapod shrimps, the difference in genome size can be said to be surprisingly large, with some species less than 2 Gb and others exceeding 40 Gb (Rutz et al., 2023). Such a huge difference is actually largely the result of the increase and decrease of repetitive sequences. For example, Yuan et al. (2021b) studied the vannamei shrimp and the Chinese shrimp (F. chinensis) and found that although they are both rich in simple sequence repeats (SSRs), they have continued to expand in independent lineages. This expansion is speculated to have occurred shortly after the genome of the shrimp ancestors had undergone differentiation, which coincided with the time of the dramatic environmental changes at the end of the Paleozoic. In the past, many people regarded microsatellite repeats as "junk DNA", but in shrimps, the large accumulation of SSRs seems to provide genome plasticity and prepare "raw materials" for subsequent adaptive evolution. Changes in the number of transposable elements (TEs) are another factor that leads to different genome sizes. For example, in the family of eusocial shrimps, the genomes of eusocial species are much larger than those of non-social species, mainly due to the accumulation of transposons. Chak et al. (2021) analyzed 33 species of pistol shrimp (genus Synalpheus) and found that the stronger the sociality, the larger the genome and the higher the TE content. It seems that the evolution of social behavior not only affects the interaction between individuals, but also indirectly promotes changes in genome structure by accelerating transposon enrichment. This also reminds us that genome expansion is not always "neutral". Sometimes, the increase in repetitive sequences may really be linked to the adaptation of species to new environments and the increase in complexity. 5.2 Gene family expansion and functional innovation In the evolution of shrimp, gene family expansion is not uncommon, and it is often related to their special physiological adaptations. By comparing the genomes of different shrimp species, we can see at a glance which gene families have expanded particularly strongly in certain lineages. For example, Penaeus vannamei has expanded a lot of genes encoding visual proteins. Zhang et al. (2019) speculated that this may be to adapt to the weak light environment on the seabed - multiple copies of rhodopsin protein can help them improve their vision in dim light. In addition, Penaeus vannamei molts frequently and has a large demand for chitinase and cuticle protein, so these related genes have also expanded in multiple copies. For example, some marine shrimps living on reefs or substrates have also expanded genes related to adhesion proteins and chitin binding proteins, which may allow them to better adhere to various surfaces. Expansion is certainly a way of adaptation, but there are exceptions. Some genes shrink or even disappear in specific environments. For example, freshwater shrimps lack some genes related to seawater ion transport, which helps them adjust osmotic pressure in low-salt environments. These expansions and contractions, put together, paint a vivid picture of the dynamic evolution of the genome in response to environmental pressures. 5.3 Whole genome duplication and polyploidization events Whole genome duplication (WGD) in animals is relatively rare in vertebrates and other groups, but has occurred in some invertebrates (such as myriapod insects). For decapod shrimps, no clear whole genome duplication events have been reported. However, there is evidence that individual species may have experienced special polyploidization phenomena. For example, stream crabs and some crayfish have chromosome doubling and parthenogenesis. A famous example is the marbled crayfish (Procambarus virginalis), whose genome is a triploid clone that has been widely invasively distributed through parthenogenesis in a very short period of time (Gutekunst et al., 2018). Although crayfish are not typical "shrimp", as a member of the decapod order, their special evolutionary events are worthy of attention. The clonal evolution and rapid spread of this genome were analyzed by Gutekunst et al. (2018), showing another facet of the plasticity of crustacean genomes. Although no similar large-scale doubling events have been found in shrimp and prawns, as the number of sequenced species increases, it is possible that evidence of WGD will be found in some ancient lineages in the future. If found, it will provide new clues for understanding the evolutionary innovation of shrimp.
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