Figure 3
Synteny conservation in the genomic regions containing CTCFL orthologs. (A) Improved continuity of the bamboo shark genome assembly Cpunctatum_v2.1 by the Dovetail Chicago, in comparison with an earlier version Cpunctatum_v1.0. The ORF sequence of the CTCFL gene was derived from the scaffold ccg_chipu00000311 through manual curation. (B) Conserved synteny involving the CTCFL gene loci between human, softshell turtle, and bamboo shark. Only the orthologs that were confirmed by molecular phylogeny inference to be shared between the scaffold ccg_chipu00000311 of the bamboo shark genome assembly Cpunctatum_v2.1 and the human chromosome region 20q13 are shown, together with their orthologs of the scaffold JH209331.1 in the softshell turtle assembly PelSin1.0. Orthology is indicated with the same vertical level of the boxes. The CTCFL orthologs are indicated with orange boxes, and the PCK1 orthologs (see C) with light green boxes. The black dots indicate scaffold ends. See Supplementary Fig. S3 for a genomic landscape for these species in which relative lengths between genes are taken into account. (C) Molecular phylogenetic tree of the PCK1 gene and its relatives. The tree was inferred with the maximum-likelihood method using 616 aligned amino acid sites. The support values at nodes indicate bootstrap values and posterior probabilities based on the maximum-likelihood and Bayesian inference in order, respectively.
