2.11 Desiccation-adaptive mechanisms of C. japonica
Two desiccation-tolerant species (including C. japonica andA. amphitrite ) were selected as foreground species, and then the
CAFE software (version 3.1) (De Bie et al., 2006) was applied to analyze
the expansion and contraction of the gene family to explore the
desiccation adaptive mechanisms of C. japonica . Multiple tree
files were constructed for the nine species using all single-copy
orthologous genes The codeml program in the PAML software (version 4.9)
(Yang, 2007) was applied to estimate the non-synonymous/synonymous ratio
(w ) to determine the positively selected genes (PSGs) of C.
japonica and A. amphitrite . Finally, gene enrichment analysis
was performed for the expanded gene families and PSGs based on GO and
KEGG databases, respectively.