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However, statistical analysis of protein domain distributions across animal genomes did identify several notable gene family expansions in octopus, including protocadherins, C2H2 zinc-finger proteins (C2H2 ZNFs), interleukin-17-like genes (IL17-like), G-protein-coupled receptors (GPCRs), chitinases and sialins (Figs 1b, 2 and 3; Extended Data Figs 4, 5, 6 and Supplementary Notes 8 and 10).a, For a larger version of panel a, see Extended Data Fig. Phylogenetic tree of cadherin genes in Hsa (red), Dme (orange), Nematostella vectensis (mustard yellow), Amphimedon queenslandica (yellow), Cte (green), Lgi (teal), Obi (blue), and Saccoglossus kowalevskii (purple).I, Type I classical cadherins; II, calsyntenins; III, octopus protocadherin expansion (168 genes); IV, human protocadherin expansion (58 genes); V, dachsous; VI, fat-like; VII, fat; VIII, CELSR; IX, Type II classical cadherins.The unassembled fraction is dominated by high-copy repetitive sequences (Supplementary Note 1).Nearly 45% of the assembled genome is composed of repetitive elements, with two bursts of transposon activity occurring 56-million years ago (Mya) (Supplementary Note 4).To explore the genetic features of these highly specialized animals, we sequenced the Octopus bimaculoides genome by a whole-genome shotgun approach (Supplementary Note 1) and annotated it using extensive transcriptome sequence from 12 tissues (Methods and Supplementary Note 2).The genome assembly captures more than 97% of expressed protein-coding genes and 83% of the estimated 2.7 gigabase (Gb) genome size (Methods and Supplementary Notes 1, 2, 3).
bimaculoides; Pfu, Pinctada fucata; Xtr, Xenopus tropicalis.Skin sampled for transcriptome analysis included the eyespot, shown in light blue.b, C2H2 and protocadherin domain-containing gene families are expanded in octopus.Enriched Pfam domains were identified in lophotrochozoans (green) and molluscs (yellow), including O. For a domain to be labelled as expanded in a group, at least 50% of its associated gene families need a corrected P value of 0.01 against the outgroup average.Some Pfams (for example, Cadherin and Cadherin_2) may occur in the same gene, however multiple domains in a given gene were counted only once.