De novogenome sequence assembly of the RNAi-tractable endosymbiosis model systemParamecium bursaria186b reveals factors shaping intron repertoire

Abstract

How two species engage in stable endosymbiosis is a biological quandary. The study of facultative endosymbiotic interactions has emerged as a useful approach to understand how endosymbiotic functions can arise. The ciliate protistParamecium bursariahosts green algae of the order Chlorellales in a facultative photo-endosymbiosis. We have recently reported RNAi as a tool for understanding gene function inParamecium bursaria186b, CCAP strain 1660/18 [1]. To complement this work, here we report a highly complete host genome andtranscriptome sequence dataset, using both Illumina and PacBio sequencing methods to aid genome analysis and to enable the design of RNAi experiments. Our analyses demonstrateParamecium bursaria, like other ciliates such as diverse species ofParamecia, possess numerous tiny introns. These data, combined with the alternative genetic code common to ciliates, makes gene identification and annotation challenging. To explore intron evolutionary dynamics further we show that alternative splicing leading to intron retention occurs at a higher frequency among the smaller number of longer introns, identifying a source of selection against longer introns. These data will aid the investigation of genome evolution in theParameciaand provide additional source data for the exploration of endosymbiotic functions.