3.6 Phylogenetic relationship and evolutionary history ofC. japonica
We compared the C. japonica genome with seven other model
species,
includingA. amphitrite , which is also a desiccation-tolerant species to
analyze the desiccation-adaptive evolution of C. japonica . Of all
the genes (30,900) of C. japonica , 23,684 genes were assigned to
12,396 gene families (Figure.5). Compared with the seven other species,
1,138 gene families were unique to C. japonica (Table 8, Figure
6). Using ORTHOMCL software, we identified a set of 968 single-copy
orthologous genes shared by eight species (Figure 6).
Phylogenetic
analysis based on single-copy orthologous genes clustered C.
japonica and P. trituberculatus into one branch, and the
differentiation time between C. japonica and P.
trituberculatus was 42.1–135.5 Mya (Figure 7). Compared with seven
other species, we identified 2,417 expanded and 2,709 contracted gene
families in C. japonica (Figure 7). The expanded gene families ofC. japonica were significantly enriched in 1,375 GO terms and 85
KEGG pathways (corrected P < 0.05).
We applied the PSMC method to estimate the demographic history ofC. japonica . The historical demographic pattern (Figure 8) shows
that C. japonica maintained a relatively stable population size,
followed by an obvious expansion, and reached their maximum effective
population size about 0.5×105 years ago.