(A) Scale map of connections between contigs in Ver_v2 suggested by the alignment of paired-end Illumina reads (insert size, ~300 bp). (A) Scale map of connections between contigs in Ver_v2 suggested by the alignment of paired-end Illumina reads (insert size, ~300 bp). Colors denote different relative coverages. Deletions are suggested by joins between distal regions in the mnd gene cluster. While deleted regions have 5× coverage, the rest of mnd has 7× coverage, indicating that deletions occur in 2/7 repeats. (B) Comparison of gene length in “Ca. Didemnitutus mandela” and Opitutus sp. GAS368. Genes <80% of the length of the Opitutus sp. GAS368 homolog are putative pseudogenes. (C) For genes without a homolog in Opitutus sp. GAS368, length is compared to their closest BLASTP hit. (D) Analysis of COG gene categories in “Ca. Endolissoclinum faulkneri,” “Ca. Didemnitutus mandela,” and Opitutus sp. GAS368, for genes that are not putative pseudogenes. Juan Lopera et al. mSystems 2017; doi:10.1128/mSystems.00096-17