2.9 Comparative genomic and phylogenetic analysis
To identify the gene families for phylogenetic tree construction, we
compared the genome assembly of C. sonnerati with other fish,
including Epinephelus lanceolatus , Plectropomus leopardus ,Epinephelus akaara , Oreochromis niloticus , Lates
calcarifer , Gymnodraco acuticeps , Pseudochaenichthys
georgianus , Cyclopterus lumpus, Danio rerio , Salmo
salar , Monopterus albus , Monopterus albus , Gadus
morhua , Oncorhynchus mykiss , and Oryzias latipes .Latimeria chalumnae was used as an outgroup. All of the proteins
were extracted and aligned to each other using BLASTP (Camacho et al.,
2009) programs (NCBI blast v2.6.0) with a maximal e-value of
1e-5. The OrthoFinder (Emms & Kelly, 2015) method was
used to cluster genes from these different species into gene families.
To reveal the phylogenetic relationships among C. sonnerati and
the aforementioned fishes, protein sequences from 678 single-copy
orthologous gene clusters were used for phylogenetic tree
reconstruction. The protein sequences of the single-copy orthologous
genes were aligned with the MUSCLE (v3.8.31) (Edgar, 2004) program, and
the corresponding Coding DNA Sequences (CDS) alignments were generated
and concatenated with the guidance of protein alignment. RAxML (v8.2.11)
(Stamatakis, 2014) was used to construct the phylogenetic tree with the
maximum likelihood method. The phylogenetic relationship of other fish
was consistent with previous studies. We used the MCMCTree program of
the PAML package (Yang, 2007) to estimate the divergence time among
species.