4.2 The Genome of F. chinensis contracted compared to other penaeid shrimps
The K-mer analysis revealed that the F. chinensis genome is 1.38 Gb in size. Compared to the genomes of other three penaeid shrimps,L. vannam ei (2.60 Gb) (X. Zhang et al., 2019), P. monodon(2.59 Gb) (Yuan et al., 2017), andM. japonicus (2.28 Gb) (Yuan et al., 2017), the genome size ofF. chinensis contracted sharply (Table 2). Although F. chinensis and L. vannam ei genomes contain a similar number of genes (25,026 vs. 25,596, respectively), the proportion of repetitive sequences in F. chinensis is markedly lower (57.73% vs. 78.00%, respectively) (X. Zhang et al., 2019). The lower repetitive sequences proportion could contribute to the genome contraction, but not be the dominant factor, because the P. monodon , which closer to F. chinensis in evolution, has a similar repetitive sequences proportion with F. chinensis (62.5%), but the genome size is also bigger (2.59 Gb) (Uengwetwanit et al., 2021).
Research suggests that genome size is under selective pressure to contract owing to constraints placed by an elevated metabolism on cell size (Hughes & Hughes, 1995; Olmo, 1983; Szarski, 1983). A similar phenomenon is observed in vertebrates. The two living groups of flying vertebrates, birds and bats, have constricted genome sizes compared with their close relatives (Hughes & Hughes, 1995). Research shows that genome size contraction preceded flight during evolution (Organ & Shedlock, 2009). Likewise,F. chinensis shrimp has a special characteristic relative to L. vannamei , P. monodon , and M. japonicus , which is migration. Same as flight, migration requires a high metabolic intensity, which closely linked with genome size (Andrews, Mackenzie, & Gregory, 2009; Vinogradov & Anatskaya, 2006). The nucleotypic theory suggests that genome size affects nucleus size and cell size (Bennett, 1971; Gregory, 2001). The cell size may further influence housekeeping dynamics, cellular metabolism, and the rate of cell division, leading to small cells with higher metabolic rates (Kozlowski, Konarzewski, & Gawelczyk, 2003). The results of gene family expansion and contraction analysis and positive selection analysis support this conjecture. The F. chinensis shrimp genome showed expanded several gene families related to cellular process and metabolic process, and genes involved in cellular process had undergone positive selection during evolution.