Intragenomic 18S Sequence Variability in the Termite Symbionts Kofoidia loriculata and Kofoidia repleta n. sp. (Parabasalia)

Kofoidia loriculata is an obligate symbiont of the desert dampwood termite Paraneotermes simplicicornis (Kalotermitidae). Its 18S rRNA genes were reported to show high sequence variability, but whether the variability was intragenomic, intraspecific, or even interspecific remained unclear. Here, we have cloned and sequenced PCR-amplified 18S genes from individually isolated Kofoidia cells. Our phylogenetic analyses indicate that two species of Kofoidia inhabit P. simplicicornis in Arizona. Both species show intragenomic 18S sequence variability, with as little as 96.4% sequence identity between clones from a single cell, while the mean interspecific pairwise identity was 92.4%. Using RT-PCR on DNase-treated cells, we also observed sequence variability among the expressed 18S rRNAs.