Bioscience Methods 2025, Vol.16, No.4, 183-192 http://bioscipublisher.com/index.php/bm 184 2 Comparative Phylogenomics in Oyster Evolution 2.1 Phylogenomic methods and datasets applied to oysters To understand how oysters evolved, it is not something that can be solved by just looking at the shell. Especially now, many studies are no longer satisfied with traditional methods. Scientists prefer to use genome-level methods for analysis, and they have indeed accumulated a lot of technology over the years. Whole genome resequencing and chromosome-level assembly sound complicated, but in fact they are just to see more clearly which genes are changing and how they are changing. Sometimes, just by looking at a few marker sites in mitochondrial or nuclear DNA, you can find obvious differences between different species (Li et al., 2021b). However, there are exceptions. The genetic changes in some lineages are not obvious, and they can only be seen by comparing them on a larger scale (Figure 1). Through these new tools, people have found that the gene families of some oysters have become very large, which may be the result of the "duplication" of certain specific genes. Some structures have also changed, and these changes seem to be related to their adaptation to the environment (Li et al., 2022). Of course, this speculation still needs more experimental evidence to support it. Whether it is sequencing technology or data analysis methods, it is now more detailed and deeper than before, providing us with a new path to study oyster evolution. Figure 1 Chromosome-level assembly of the estuarine oyster Crassostrea ariakensis genome (Adapted from Li et al., 2021b) Image caption: a Estuarine oyster (photo by Lumin Qian). b Hi-C interaction heatmap showing 10 chromosomes of the estuarine oyster. c CIRCOS plot showing 10 chromosomes. d Summary statistics of the genome assembly (Adapted from Li et al., 2021b)
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