Fig. 1
From: The genomic and functional landscapes of developmental plasticity in the American cockroach
Orthology and genome evolution of Blattodea. a Orthology assignment of four blattodean species and eight other representative insect species (Supplementary Table 6). Bars are subdivided to represent different types of orthology clusters as indicated. Universal groups represent common gene families across all species analyzed, but absence in at most one genome is tolerated; of them, “single-copy” tolerates absence or duplication in a single genome, while “multiple-copy” indicates other universal genes. “Blattodea only” indicates unique presence to the blattodean lineage and in at least three genomes. “Specific” groups indicate specific presence or duplication in only one species. “Homology” indicates partial homology detected with E < 10−5 but no orthology grouped. Remaining orthologs were assigned to “Present at half of species” or “Patchy”, depending on whether presence is in at least six genomes or not. The phylogeny was calculated using maximum-likelihood analyses of a concatenated alignment of 538 exactly single-copy proteins. The tree was rooted using the sister clades of Blattodea and Orthoptera species as described previously70. Bootstrap values based on 100 replicates are equal to 100 for each node. b Distribution of sequence identities. The boxplots delineate the interval between the first and the third quartiles of the identity distribution between P. americana and one indicated blattodean species. Notch indicates the median value. Amino acid sequence identity was calculated based on multiple alignment of each universal single-copy ortholog (5911 in total) in four blattodean species. The red dashed line indicates the median value within Periplaneta species (96%). c Comparison of sequence identities on each ortholog cluster. A total of 7640 1:1:1 orthologs were identified among P. americana, B. germanica, and Z. nevadensis. Each dot represents such an ortholog. Value on x-axis indicates the sequence identity between P. americana (Pame) and B. germanica (Bger), while value on y-axis indicates that between P. americana and Z. nevadensis (Znev). Red line indicates the smoother of a locally weighted regression, with the coefficient of determination as 0.99999. Dashed line indicates positions where the sequence identity between P. americana and B. germanica is identical to that between P. americana and Z. nevadensis
