Figure 4.

Syntenic cluster analysis among human FUNDC1 and FUNDC2. This analysis was carried out to evaluate the hypothesis that two FUN14 domain-containing proteins in vertebrates result from WGDs in the vertebrate ancestor, as opposed to simple tandem duplications. Human FUNDC1 and FUNDC2 (labeled in red) localize in two regions with a 100-Mb distance on the same chromosome (X) (Supplementary Table 2). The online pipeline of the Synteny Database (Catchen et al., 2009) was modified in this analysis. Paralogous proteins in the human genome were retrieved through BioMart and the paralogous groups were then filtered through outgroup anchoring. Lancelet Branchiostoma floridae was used as an unduplicated outgroup (see Materials and Methods). Finally, through a manually sliding window analysis, conserved syntenic clusters (the neighboring genes of FUNDC1 and FUNDC2 keep their relative positions and orders) were detected between the two human genomic regions, which individually contain FUNDC1 and FUNDC2. Colored lines between two paralogs denote different syntenic blocks. Nine gene pairs are shared in the paralogous syntenic clusters, in which three gene pairs are recorded in the Ohnologs database (Singh et al., 2015), which houses ohnologs—paralogous genes retained from WGD—in six vertebrate genomes.