International Journal of Marine Science, 2025, Vol.15, No.3, 154-166 http://www.aquapublisher.com/index.php/ijms 155 With the development of genomics, scientists began to examine shrimp growth and reproductive traits from the perspective of genomic evolution. Genome evolution research can reveal key genetic variation and evolutionary drivers that affect traits, providing a theoretical basis for genetic breeding. In recent years, the whole genome sequences of various shrimp species have been deciphered successively, and the acquisition of high-quality genome maps has made comparative genome and evolutionary analysis possible. Studies have shown that there are a large number of species-specific genes and tandem repeat genes in the shrimp genome, which are the characteristics of the formation of shrimp during the long-term evolution (Tan et al., 2019). Some progress has been made in the evolutionary research on growth and reproduction-related genes: comparing the genomes of different species, it was found that the significant expansion of the visual and motor-related genes of shrimp may be related to the evolutionary adaptation of their benthic lifestyle; for example, multiple genes on the ecdysterone pathway in the Pacific white shrimp genome have undergone positive selection, explaining the genetic basis of their frequent molting and rapid growth (Zhao et al., 2021). In addition, simple sequence repeats (SSRs) are present in large quantities in the shrimp genome and have been found to drive the plasticity and adaptive evolution of the shrimp genome. 2 Progress in Genomics o Shrimp 2.1 Milestones and technological evolution of genome sequencing of shrimp species Over the past decade, genome sequencing of shrimp species has achieved a leap from scratch. In 2014, Chinese scientists took the lead in deciphering the genome sketch of Chinese prawns (Fenneropenaeus chinensis), opening the prelude to crustacean genome research. Subsequently, the genotype composition of the Pacific white shrimp released in 2019 was the first high-quality reference map for shrimp genomes. The genome is about 1.66 Gb in size, encodes about 25 596 genes, and Scaffold N50 reaches 605 Kb (Pérez-Enríquez et al., 2024). The study found that a major feature of the shrimp genome is its high repetition: simple tandem repeats account for more than 23.93% of the genome, which is the highest content among the measured species (Yuan et al., 2021). Huge repeat sequences and complex genomic structures once hindered the assembly of shrimp genomes, but with the evolution of high-throughput sequencing technology, this problem has gradually been overcome. In the early stage, the hybrid strategy of second-generation sequencing (Illumina) combined with BAC library was adopted to barely construct the shrimp genome framework. Entering the era of third-generation sequencing, the high-yield PacBio/ONT long-read and Hi-C assistive technologies have been applied to shrimp genome assembly. In terms of freshwater large shrimp, the high-quality reference genome of Macrobrachium rosenbergii has also been released, providing a basis for studying crustacean gender decisions, etc. 2.2 Genome annotation and functional annotation methods Obtaining genomic sequences is only the first step, and it is more critical to accurately annotate genes and functional elements in the sequence. Annotation of shrimp genomes usually adopts a multi-strategic approach: on the one hand, alignment of homologous sequences can predict coding regions and conservative genes (e.g., aligning known crustacean gene sequences with newly assembled genomes); on the other hand, evidence-based support is supported by transcriptome data, exon-intron structures and transcripts are determined by aligning mRNA/cDNA sequences (Li et al., 2012; Wei et al., 2014). For large genomes such as Pacific white shrimp, researchers comprehensively used Ab initio prediction, homologous alignment and transcriptome assembly to annotate genes. The results showed that the genome of Pacific white shrimp contains about 25,000 protein-encoding genes. In addition to coding genes, non-coding RNAs, repeat sequences and regulatory elements in the genome are also annotated and classified through specialized software. In terms of functional annotation, using public databases (such as NCBI Nr and Swiss-Prot) to perform homologous search of predicted proteins can be conferred on preliminary functional annotation of genes. In addition, the distribution of gene roles in biological processes, molecular function and cellular components can be understood through Gene Ontology (GO) classification and KEGG pathway analysis. 2.3 Genomic databases and information resources (such as NCBI, ShrimpBase, etc.) As multiple shrimp genomes were measured one after another, a large amount of data was stored in public
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