International Journal of Marine Science, 2025, Vol.15, No.2, 53-64 http://www.aquapublisher.com/index.php/ijms 55 2.4 Challenges in analyzing species relationships Analyzing the species relationships of groupers is a relatively difficult task because many different species of groupers look very similar and are easily confused (Aziz et al., 2016; Ayu et al., 2024; He et al., 2024). Although molecular biological methods (especially DNA barcoding of the COI gene) have improved the accuracy of species identification, there are still difficulties and discrepancies between morphological and molecular data (Aziz et al., 2016; Loh et al., 2024). Some genera are not monophyletic groups, and the taxonomic status of closely related species requires more genetic markers and larger sample sizes for more in-depth research (Craig and Hastings, 2007; Wang et al., 2022; Loh et al., 2024). 3 Progress in Grouper Genomics 3.1 Milestones in grouper genome sequencing Great progress has been made in grouper genomics, from the earliest preliminary assembly to the current high-quality chromosome-level genome. The genome of the yellow grouper (Epinephelus coioides awoara) has been assembled at the chromosome level, and 99.76% of the genome sequence is fixed on 24 pseudo-chromosomes, which provides a good resource for studying the population genetics, adaptive evolution and speciation of grouper (Zhang et al., 2024). In addition, the genome of the giant grouper (Epinephelus coioides lanceolatus) has also been sequenced with high precision, and the study has also discovered some key gene families, such as antimicrobial peptides, which are very important for disease resistance and aquaculture (Wang et al., 2019). These advances have laid a solid foundation for basic and applied research on groupers. 3.2 Technologies and tools used The progress in grouper genomics has been mainly achieved through advanced sequencing technologies. Long-read sequencing platforms have played a very important role in genome assembly and complex regional analysis, which is mainly carried out through PacBio's single-molecule real-time (SMRT) sequencing technology (Wang et al., 2019; Cao et al., 2024; Zhang et al., 2024). Hi-C chromosome conformation capture technology can assemble the genome to the chromosome level, greatly improving the completeness and accuracy of researchers in the process of genome research (Zhang et al., 2024). Next-generation sequencing (NGS) combined with full-length transcriptome sequencing can better study gene expression and regulation. In the genetic study of hybrid grouper, we can better understand hybrid vigor and related genes (Cao et al., 2024). 3.3 Comparative genomics with other teleosts With the completion of the high-quality genome of grouper and the advancement of alignment and annotation methods, comparative genomics has become more widely used. By using tools and frameworks for long-read sequencing data, comparative genomics can help us discover sample or population-specific gene sequence and structural variations, even variations in complex and repetitive regions (Wang et al., 2020; Khorsand et al., 2021). Comparing the genomes of bony fish with those of other vertebrates can help us identify conserved coding regions, non-coding regions, regulatory elements, and evolutionary dynamics, all of which help to gain a deeper understanding of the grouper genome and its diversity (Thomas et al., 2003; Armstrong et al., 2019). These comparative analyses are very important for understanding the genomic basis of adaptation, speciation, and trait evolution in groupers. 4 Genome Structure and Variation 4.1 Chromosome structure, size and gene content The chromosome structure of groupers is well preserved, and most species have 24 chromosomes. Many grouper species have completed chromosome-level genome assemblies, such as yellow grouper (Epinephelus coioides awoara, 984.48 Mb), brown marble grouper (E. fuscoguttatus, 1 047 Mb) and giant grouper (E. lanceolatus, 1.06 Gb~1.086 Gb) (Zhou et al., 2019; Yang et al., 2021; Zhang et al., 2024). These genomes are well assembled, with scaffold N50 values generally exceeding 40 Mb, and more than 98% of the sequences are fixed on chromosomes. These species are expected to have 24 000 to 25 000 protein-coding genes, and functional annotations are also high, exceeding 90% (Yang et al., 2021; Zhang et al., 2024). Some gene families, especially those related to immunity and growth, have been expanded (Zhou et al., 2019; Wang et al., 2022).
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