A paradox: rapid evolution rates of germline-limited sequences are associated with conserved patterns of rearrangements in cryptic species of Chilodonella uncinata (Protista, Ciliophora)

Abstract

Some of the most extreme genome wide rearrangements are found in ciliates, which are unique in possessing both germline micronucleus and somatic macronucleus in every cell/organism. A series of DNA rearrangement events, including DNA elimination, chromosomal fragmentation, gene unscrambling and alternative processing, happen during macronuclear development. To assess the molecular evolution of macronuclear and germline-limited sequences in different cryptic species of Chilodonella uncinata, we characterized the actin, α-tubulin and β-tubulin genes in the micronucleus and macronucleus genomes of USA-SC2 strain and compared them with other strains (i.e. cryptic species). Three main results are: (i) rearrangement patterns between germline and soma are conserved for each gene among the cryptic species of C. uncinata; (ii) in contrast, the germline-limited regions are highly divergent in sequence and length among the cryptic species; (iii) pointer shifting is frequent among the cryptic species. We speculate that pointer sequences may serve as the buffer between the conserved macronuclear destined sequences and rapidly-evolving internal eliminated sequences. The data combined with previous studies demonstrate the plasticity of gene rearrangement among different groups of ciliates and add to the growing data for the role of genome rearrangements in species differentiation.

Genome analyses of the new model protist Euplotes vannus focusing on genome rearrangement and resistance to environmental stressors

“…Excision of IESs is generally not precise in Tetryhmena while must be precise in Paramecium , Chilodonella , Oxytricha and Euplotes . Moreover, gene scrambling is widespread in Oxytricha (Chen et al, ) and Chilodonella (Maurer‐Alcalá et al, ; Zhang, Wang, Katz, & Gao, ), but not frequently observed in Tetrahymena , Paramecium and Euplotes . As to the Euplotes in the present study, which is most closely related to Oxytricha based on morphology and phylogeny, its chromosomal fragmentation is similar to Oxytricha (Figure ); however, its DNA elimination resembles Paramecium (Figure ).…”

Comparative Genomics Analysis of Ciliates Provides Insights on the Evolutionary History Within “Nassophorea–Synhymenia–Phyllopharyngea” Assemblage

“…Cyrtophorians are characterized by a glabrous dorsal side and prominent cytopharyngeal basket composed of a large number of microtubules (Lynn, 2008). Although several cyrtophorians have been studied recently (Chen et al, 2016;Pan et al, 2016;Zhang et al, 2018), the systematics of this group remains ambiguous. Therefore, the class TABLE 1 | Taxonomic schemes for the classification of 10 species ciliates in four systematic schemes.…”

Further analyses on the evolutionary “key‐protist”Halteria(Protista, Ciliophora) based on transcriptomic data

“…2017; Wang, Chen, Sheng, Liu, & Gao, 2017;Wang, Zhang, et al, 2017;Xiong et al, 2016;Yan et al, 2018;Yan, Rogers, Gao, & Katz, 2017;Zhang, Wang, Katz, & Gao, 2018;Zhao, Wang, Wang, Liu, & Gao, 2017;Zhao, Yi, Warren, & Song, 2018). Although these topics have been studied for hundreds of years, there are still many unresolved issues, such as the considerable discordance between morphologies and molecules, which can be caused by convergent morphologies, cryptic species, plastic phenotypes or life-cycle stage variation (reviewed in Lahr, Laughinghouse, Oliverio, Gao, & Katz, 2014).…”