International Journal of Marine Science, 2025, Vol.15, No.1, 35-44 http://www.aquapublisher.com/index.php/ijms 37 2.2 Traditional phylogenetic framework based on morphology and molecular markers For many years, the study of phylogenetic relationships of shrimps has continued to advance. Research based on molecular data generally supports that the major suborders of the decapod order are monophyletic groups. For example, the latest shrimp phylogenetic tree constructed by large-scale anchored hybrid enrichment shows that each shrimp branch (such as shrimps, true shrimps, crayfishes, etc.) shows a clear monophyletic evolutionary branch. Wolfe et al. (2019) used 410 gene fragments from 94 representative species of decapods to reconstruct the most comprehensive decapod phylogenetic tree to date, which not only confirmed the evolutionary relationship between traditional suborders and superfamilies, but also inferred that the crown group of decapods originated in the Late Ordovician, and the main living lineages rapidly differentiated in the Triassic-Jurassic period. This period coincided with the end-Permian mass extinction event, and the huge environmental changes may have driven the radiation evolution of shrimps. 2.3 Challenges and controversies in solving the evolutionary relationship of decapods Although the high-level classification of most shrimps has been basically clarified, some more detailed relationships below the family level are still being explored. For example, the position of mud shrimps (formerly classified in the superfamily Thalassinidea) has caused a lot of controversy in the past. Later, researchers finally figured out that this group of shrimps should be divided into two independent lineages, the order Thalassinidae and the order Thalassinidae, by comparing mitochondrial genomes (Lin et al., 2012). Of course, it is not only a classification problem, the species diversity of shrimps themselves is also quite amazing. Take the Alpheidae family as an example. The pistol shrimps in it have all kinds of lifestyles, from solitary to truly social groups. This complex behavioral change provides a particularly good example for studying evolution and ecological adaptation. 3 Progress in Decapod Shrimp Genome Resources 3.1 Recent genome sequencing projects and major data sets For a long time, crustacean genomes have been a headache to sequence, mainly because their genomes are large and complex, with a lot of repetitive sequences (Yuan et al., 2021a). This was basically the case before the mid-2010s. However, things have changed in the past five years. Many whole genome projects for economically and ecologically important shrimp species have been launched internationally, finally pushing shrimp genome resources from zero to a new stage. In 2019, Zhang et al. published the first high-quality shrimp genome, Penaeus vannamei, with a total genome length of approximately 1.66 Gb and 25 596 predicted coding genes. Interestingly, in this genome, simple repeat sequences (1~6 bp tandem repeats of SSR) accounted for more than 23.9%, the highest among all species measured at the time. Such a high repetition rate also reveals that the shrimp genome is a bit special, leaving a lot of room for imagination for future studies of their adaptive evolution. 3.2 Development of transcriptome and mitochondrial genome databases Since then, reference genomes of many important shrimp species have been deciphered and released, including the chromosome-level genome of Japanese shrimp (Marsupenaeus japonicus) (Kawato et al., 2021), the chromosome-level genome of black tiger shrimp (Penaeus monodon), the improved genome of Chinese shrimp (Fenneropenaeus chinensis) (Wang et al., 2022), and the highly continuous genome of Indian shrimp (Penaeus indicus). Most of these studies used third-generation long-read sequencing combined with Hi-C-assisted assembly, which significantly improved the assembly quality. For example, the Japanese shrimp genome constructed by Ren et al. (2022) is 1.24 Gb in length, with an N50 of 13.4 Mb, and identified approximately 26 381 genes; the giant tiger shrimp genome released by Uengwetwanit et al. (2021) assisted in the location of growth-related genes. For the shrimp Penaeus vannamei, Peng et al. (2023) further used third-generation sequencing and Hi-C technology to assemble its genome to the chromosome level, with the full length increased to 1.87 Gb and the scaffold N50 increased by two orders of magnitude to 39.7 Mb. 3.3 Limitations and future needs of decapod genome data Although the current level of genome assembly has been greatly improved compared to the past, after all, the
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