2.8 Comparative genomic analyses and testing for genomic
selection
We performed an extensive orthologous gene comparison of C.
japonica with eight other model species with genome datasets, includingChionoecetes opilio (GCA_016584305.1), Hyalella azteca(GCA_000764305.3), Penaeus vannamei (GCA_003789085.1), P.
trituberculatus (GCA_017591435.1),Drosophila
melanogaster (GCA_003401745.1),Amphibalanus
amphitrite (GCA_019059575.1), and Daphnia magna(GCA_003990815.1). We downloaded the protein sequences from the
National Center for Biotechnology Information database. Subsequently, we
extracted the orthologous groups using the ORTHOMCL software (version
2.0.9) (Chen et al., 2006) and filtered the BLASTP results with default
parameters. The single-copy orthologous genes shared by all nine species
were further aligned using the MUSCLE software (version 3.8.31) (Edgar,
2004), and conserved sequences were extracted from each concatenated
nucleotide sequence using the Gblocks software with parameter −t=c. We
performed 1000 nonparametric bootstrap replicates for the optimal
GTRGAMMA substitution model of all concatenated nucleotide sequences,
and then a phylogenetic tree of the nine species was constructed using
the RaxML software (version 8) (Stamatakis, 2014). The divergence times
of the nine species was estimated using the r8s software, and fossil
evidence was used to calibrate the divergence time. Furthermore, the
CAFE software (version 3.1) (De Bie et al., 2006) was applied to analyze
the expansion and contraction of the gene family, and P < 0.05
was used to indicate remarkably changed gene families. Gene enrichment
analysis was performed for the extended and contracted gene families
based on GO and KEGG databases, respectively.