Taxon annotated GC-coverage plot of the primary genome assembly of Culicoides punctatus
Circular representation of cCpun genome using Circos v0.69 (Krzywinski et al. 2009)
To enhance visualization the scaffolds were size sorted and concatenated into a pseudomolecule. The alternating grey and white strips highlight the scaffold borders. Inwards, the first, second and third circle are colour coded according to COG functional categories and represent a) the complete cCpun protein coding genes, b) the core genes between the four Amoebophilaceae genomes presented in Figure 1A, and c) the cCpun unique genes. In the fourth circle we show the genomic location of the genes coding for the Afp-like (magenta) and type IX (red) secretion systems as well as the DUF1703 gene paralogs. Finally, the two line plots represent genome coverage and GC% content across cCpun genome (1kb sliding window) respectively. An orange line indicates the mean coverage (90X) of the draft assembly.
cCpun is a near complete genome
BUSCO completeness assessment results for cCpun draft genome in comparison to the other Cardinium genomes and A. asiaticus. The Results are based on the presence or absence of 148 single-copy universal bacterial markers.
Repeat-content comparison across the five Amoebophilaceae genomes
Mummer self-plots representing sequence repeat density in the five Amoebaphilaceae genomes. Each dot represent a repeat (blue=direct) and (red=inverted) of at least 200bp and 95% similarity.
Pairwise similarity (lower right) and identity (upper left) matrix of the 24 DUF1703 protein paralogs identified in the genome of cCpun
Cardinium carbonic anhydrase homologs
Maximum likelihood phylogenetic placement of cCpun and Ca. Paenicardinium endonii (cHgTN10) carbonic anhydrase (CAs) protein sequences compared with their closest homologs in the Genbank database. Members from the four clades forming the beta-class of CAs are presented. The positions of the Cardinium homologs and the CA homolog identified in Rickettsia (RiCNE) endosymbionds in biting midges are indicated in purple and red respectively. Phylogenetic relationships were inferred using IQ-TREE v1.6.6 (method: automated best model selection).