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.